# HG changeset patch # User iuc # Date 1571259475 14400 # Node ID b7b1c8bf7ae027fb143d26812df20bdcd2f12d0b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5" diff -r 000000000000 -r b7b1c8bf7ae0 est-abundance.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/est-abundance.xml Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,65 @@ + + Bayesian Reestimation of Abundance with KrakEN + + macros.xml + + + topic_3174 + topic_3697 + + + operation_2238 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + `_. + ]]> + + diff -r 000000000000 -r b7b1c8bf7ae0 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,17 @@ + + 2.5 + @TOOL_VERSION@+galaxy0 + + + bracken + + + + echo @WRAPPER_VERSION@ + + + + 10.7717/peerj-cs.104 + + + diff -r 000000000000 -r b7b1c8bf7ae0 test-data/NC_003198.1_1kb.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_003198.1_1kb.fasta Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,14 @@ +>NC_003198.1 Salmonella enterica subsp. enterica serovar Typhi str. CT18, complete genome +AGAGATTACGTCTGGTTGCAAGAGATCATAACAGGGGAAATTGATTGAAAATAAATATATCGCCAGCAGC +ACATGAACAAGTTTCGGAATGTGATCAATTTAAAAATTTATTGACTTAGGCGGGCAGATACTTTAACCAA +TATAGGAATACAAGACAGACAAATAAAAATGACAGAGTACACAACATCCATGAACCGCATCAGCACCACC +ACCATTACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG +CCCGCACCTGAACAGTGCGGGCTTTTTTTTCGACCAGAGATCACGAGGTAACAACCATGCGAGTGTTGAA +GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATTCC +AGGCAAGGGCAGGTAGCGACCGTACTTTCCGCCCCCGCGAAAATTACCAACCATCTGGTGGCGATGATTG +AAAAAACTATCGGCGGCCAGGATGCTTTGCCGAATATCAGCGATGCCGAACGTATTTTTTCTGACCTGCT +CGCAGGACTTGCCAGCGCGCAGCCGGGATTCCCGCTTGCACGGTTGAAAATGGTTGTCGAACAAGAATTC +GCTCAGATCAAACATGTTTTGCATGGTATCAGCCTGCTGGGTCAGTGCCCGGATAGCATCAACGCCGCGC +TGATTTGCCGTGGCGAAAAAATGTCGATCGCGATTATGGCGGGACTCCTGGAGGCGCGTGGACATCGCGT +CACGGTGATCGATCCGGTAGAAAAACTGCTGGCGGTGGGCCATTACCTTGAATCTACCGTCGATATCGCG +GAATCGACTCGCCGTATCGCCGCCAGCCAGATCCCGGCCGATCACATGATCCTGATGGCGGGCTTTACTG diff -r 000000000000 -r b7b1c8bf7ae0 test-data/NC_003198.1_simulated_R1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_003198.1_simulated_R1.fastq Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,180 @@ +@NC_003198.1-90/1 +AATAAAAATGACAGAGTTCACAACATCCATGAACCGCATCAGCACTACCACCATGACCACCATCACGATTACTACAGGTAACTCTGCGGGCGGACGCGTA ++ +@CCF1FFF2HHHF@29I)IJIHIGIJGJE?CHJJBJGJHGHFJJH#J>2G0IJI#EHD=JFDDACF#GCE=J#;FC>DEA5F##D0B>CD9##CAA>B5D +@NC_003198.1-88/1 +TCATAACAGGGGAAATTTATTGAAATTAAATATATCGCCAGCAGCACATGAACAGGTTTCGGACTGTGATGAATTTAAAAAGTTATTGACTTCGGCGCTC ++ +CCCFDFFBDHDHHJF#2#H#CDECCDB>DC##DAD##? +@NC_003198.1-86/1 +GGCGATACGGCGAGTTGATTCCGCGATATCGACGGTAGATTCAAGGTAATGGCCCACCGCCAGCAGTTTTTCTACCGGATCGATCACCCTGAGGCGAAGT ++ +@CCFFF?DCHCH+IJ#GIJHICHGHHJHGGEIJCIGJJJ?GJIGHHGJ=GDJII??F#E>C>=EDCDAADCC#9?C#D#9D#>C +@NC_003198.1-84/1 +CACAGAAAAAAGCCCGCACCTGAACAGTTCGGGCTTTTTTTTCGATCTGAGATCACGAGTTAACAAGCATGCGAGTGTTGAAGTACTGCAGAACATCAGT ++ +@CCFFFDF?DEHA(?#->#;#CD:CA>@D +@NC_003198.1-82/1 +CCGGGCACTGACCCAGCAGGCTGATACCATGCAAAACATGTTTGATGTGAGCGAATTTTTGTTCGACAACCATTTTCAACCGTGCAACCCAGTATCCCGG ++ +CC@+DFDFHHGDHHIIIJGIFJIAJ#I7JIIHDJHIIJAFHIIG:?#I#GFCB4F=:#AJGIDJIJDDHFIBADGADH@EAD#DECD#C##>#A:D@D?, +@NC_003198.1-80/1 +ATAATCGCGAGCGACATTTGTTCGCCGCGGCAAATCAGCGCGGCGTTGATGCTATCCGGGCACTGATCCAGCAGTCTGATAACATGCAAAAAATGTTTGA ++ +C@CDBFFD:F#HH#BBGJI!JIIIBJ!GHDFCI>IJIFAIIAHDBIGII?HIIBCJ?BAHFGJ>HE(CJ@2ECE!DBCB=D#FB@;@CCC<#<2>#D@AC +@NC_003198.1-78/1 +CAGAAAAAAGCCCGCACCTGAACAGGGCGGGCTTTTTTTTCGACCAGAGATCACGAGGTAACAACCATGCCAGAGTTGAAGTTCGGCGGTACATCAGTGG ++ +@7@FFFFDFFFHDJJJIBJIJGIIA#IJIJJ*JE#IJJJDBBJGJICHJBD5>@C#D:CDD#B> +@NC_003198.1-76/1 +GCGAAAATTACCAACTCTCTGGTGGCGATTATTTAAAATACTATCGGCGGCCAGGATGCTTTGCCGACTATCAGCGGTGCCGAACATTTTTGCTCTGTCC ++ +?:##C!H>CBEDDB#F#B2<##BCDC##, +@NC_003198.1-74/1 +GAGGTTACAACCATGCGAGTGTTGTAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGCTATTATGGAACGCAATTCCAGCC ++ +B1C(F#FBHHHHHJJGJGIEJ@JH#G1AC>BJAJJJJJJJHJIGIIJIGHDHJ@IH5FFIEDCD@H=#E#=(#?CDD(#?DA#DCDBDB#C +@NC_003198.1-72/1 +CGCAGAAAACGTTCTGCATTTGCCACGGATGTACCGCCGAACTTCAACACTCGCATGGTTGTTACCTCGTCGCCTCTGGTCACAAAAAAAGCTCGCTCAG ++ +BCCFFFDFHHHH:BIEIIJEJHJECI#GJI+FEI?BFGJE@IJCJDHGJGIJ#F;?)?GIIH;8CABGH?###I?F=F@;A##BCB>#CA@#D#D +@NC_003198.1-70/1 +CCCGGCTGCGCGCTGGCAAGACCTGGGAGCAGGTCAGAAAAAATACGTTCGGCATCGCTGATATTCGGCAAAGCATCCTGGCCGCCGACAGTTTTTTCAA ++ +@CC?FFDFH#DFHJF@JEF1#IHID#IGJJDCG#EEJIJHIJED:JDD@B=;J#@HC93#ED#B;CC?@D#CCC#DBB>DEB +@NC_003198.1-68/1 +AAGTTCGGCGGTACATCAGTGGTAAATGGAGAACGTTTTCTGCGTGTTCCCGATATCCTGGAAAGCAATTTCAGGCAAGGGCAGAGACCGAATTCACTTT ++ +CB:FFFADDHF;>IJIHJJHJI#JIIJJ#JCJGEIDJJICGJDIGCBJ#AFIIFHD#GC3DFJIIF.HCG#JFBD:DF3D#CCE##;#DC:#####D#D, +@NC_003198.1-66/1 +TAACCAATATAGGAATACAAGACAGACAAATAAAAATGACAGAGTACACTACATCCATGAACCGAATCAGCATGACCTCCCTTACCTCGATCACCATTAC ++ +@B@DFFFDD@HGBEHI#+JIJIGIJIJ?+CIGJJJIIDJJGEFHIJAIJ#CIGHDEA9GCC=H8#DHHGEF;#(FCI#?F#CDC>##C(CDBDCC##ADD +@NC_003198.1-64/1 +CCAGCAGGCTGATACCATGCAAAACATGTTTGATCTGAGCGAATTCTTGTTCGACAACCATTTTCAACCGTGCACGCGGGATTTCCGGCAGCGCGCTGGC ++ +@8CFFFF@GHF+HFIJIIBGII@I?IJJIIFJIDGI@DIIC#IJE@IJJJ@EFDJGJJCDEH?=JGH9#DG=DC(HDEECD#E#ADC>D#D9D#@CC3DC +@NC_003198.1-62/1 +GCCTCCAGGAGTCCCGCCATAATCGCGATCTACATTTTTTGGTCACGGCAAATCAGCGCGGCGTTCAAGCTATCCGGGCACTGAACCAGCAGGCTGATAA ++ +C@=FFDDFHDGHHBHGEJC6JGDHBHEGJJ#I?AIIGJDF#I#JJGA9@F@'IEGJJICIGCDHE#C#HFBHABE;HJA,AC;5#D#FCBD+D5E@9?A, +@NC_003198.1-60/1 +AGAATATCGGCAACACGGAGAAAACGTCCTGCATTTGCCACTGATGTACCGCCTAACTTCAACACTAGCATGGTTGTCACCTCGTGCTATCTGGTCGACA ++ +??#DFFFFDG@:HJIJ@2JEJJHJ*EI!HJJIAJ0GICHGHD?#(AAIAIH.DJJE#FA7EDAD@B;#FECB.DB;#D#?ADAEC@AD#D +@NC_003198.1-58/1 +GTAATGGCCCACCGCCAGCAGTTTTTCTACCGGATCGATCACCGTGATGCGATGTCCACGAGCCTCCACGAGTCCCTCCATAATAGCGGTCGTCATTATT ++ +B@CFFDDFHHGFHJBACAJ?JIGGD#JHJJFC?#BD?#F#HJEGIFIJHH#F@DJEDG#@DCDECE#DGBDBB8#5DD#AA5#DCD:#C< +@NC_003198.1-56/1 +ACAGAGTACACAACATCCATGAACCGCATCAGCACCACCACCACTACCACCATCACCATTACCACAGGTAACGGTTCGGGCTGACGCGTACGGGATACAC ++ +C@CFDF?FD#HF?4JI;JE3IEHIIJJ9EII9J?JF)JEDJBI#DCIF>JGI?JCIG9JJID#IFH8FECJCEDC#E;C#5HD@E#5B=#?#B>E###DC +@NC_003198.1-54/1 +CGTGCAATTACTTTAACCAATATAGGAATACAAGACAGACAAATAAAAATTACAGAGTACACAACATCCATGAACCGCATCAGCACCACACCCATTACCA ++ +@C#DFF##HHCHGIH@EE9F@ABBCD###A2D@D:C#? +@NC_003198.1-52/1 +GTGCGGGCTTTTTTTTCGACCGGAGCTCAGGAGGTAACAACCATGCGAGTGTTCAACTTCGGCGGTACATCAGTTGCAAATGCCGAACGTTTTCTGCGAG ++ +@?@DFDFF#AGCIBG?HEHJA#IF#?FF#AD=C7>BA@CCD+E>BBB#E##4#DD2#@D#D +@NC_003198.1-48/1 +TTACCAACCATCTGGTGGCGATGATTGAAAAAACTATCGGCGGCCAGGATCCTTTGCCGAATATCAGCGATGCCGGACGAATTTTTTCAGACCAGCTAGC ++ +CBCFFFF3HG7G=IJBJJJFIAJIIIGJH9JGIJJ?IIBD8DIAJGFICE#JGJDI=IAGEJIHJDHJI4GJJHGHG@#DCGBD#DJ=#3FAI?HGDAE;B5;?DDH?FHC:CECC?CD?C?CBCA<, +@NC_003198.1-44/1 +ACAAGACAGACAAATAAAAATGACAGAGTACACAACATCCAAGAACCGCATAAGCACCACCACCATTACGGCCATCACCATTACCACAGGCAACGGTGCG ++ +C@CAFFDFGB+FH2G9GJJEGJC)=IJIH9IGF#JH*@##&G#?F:FHD::#C>#ABDDD@?D:BCD#DC>;?CD#E@DEA +@NC_003198.1-40/1 +TGAGCGAATTCTTGTTCGACAACCATTTTAAACCGTGCAAGCGGGAATCCCGGCTGCGCGCTGGCAAGCCTTGCGATCAGGTCAGAAAAAATACGTTCTG ++ +B@?+?DFFHHHHBIII#IAIJ+BD:DAD#B +@NC_003198.1-38/1 +CAGAAAACGTTCTGCATTTGCAACTGATGTGCAGCCGAACCTCAACACTCGCATGGTTCTTGCCTCGCGATCTCTGGTCGCAAAAAAAGCCCGCAATATT ++ +B;?FFF=FHFFHDJFJIHHIJ#JJGI9?GJ#J#BIJIIIG#JFCJI*G9G=JGJJJGJ#JJ#JJAEI#>CC>BHC>CDED)#DDHCCCACC>CB;####: +@NC_003198.1-36/1 +TGAAAATAAATATATCGCCAGCAGCACATGAACAAGTTTCGGAATGTGATCAATTCAAAAATTTATTGACTTACGCTGGCAGATACTTTTACCAATATAG ++ +C=CF=FDAGHDHHJGB?JIIFJIJJIEHFJIJIHFF!=@CHCIE#:#C8CG?CDAFA?C#BDE9@@D?C#D>>CD@D +@NC_003198.1-32/1 +GCTATCCGGGGACTGACCCAGCAGGCTGATACCATGTAAAACATGTTTGATCTGAGCGAATTCTTGTTCGACAACCATTTTCAACCGTGCAAGCGGGAAT ++ +@@CFFBFFHH#HHJIJIGJGHJJIJG#HIIDJJJIG#IBH@B9IJIGH;?; +@NC_003198.1-30/1 +GGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATTCCAGACAAGTGCAGGTTGCGAACGAACTTTCCGCCCCCGCGAGAATTACC ++ +?CD>GG>IIJ?IFHHJ#DJ'?FDJDIEHJJJGI#H8EIH#FIGJC>FCDECE#ECBCF#CDF#B#CCBA>B#43#C@ +@NC_003198.1-26/1 +TGTGCAAGCGGGAATCCCGGCTGCGCGCTGGCAAGTCCTGCGAGCACGTCAGAAAAAATACGATCGGCATCGCCGATATTCGGCAAAGCATCCAGGGCGC ++ +#CCF?FD>F-FHACBJJFHHI:#IHI?JGJGFIJJIJ#J(9@#BFA#BGGI2HII*BIIGG>#@8H#IHH#J##;@>>DEEBFB;CCCB@-#C#?C#?CD +@NC_003198.1-24/1 +CGGCATCGCTGATATTCGGCAAAGCATCCTGGCCGCCGATAGGTTTTTCAATCATCGCCACTAGATGGTAGGTAATTCTCGCGTGGGTGGATATGACGGA ++ +@C=FFFFFFHFHH+JGGIJ8IIEFIJHJIJF?GGIAJFJBJ<#G@JJGGIH7CJEJIIICG#E#E@=DE#ED3E5>C#F#DC<#ADH#CDB#D##?>?D, +@NC_003198.1-22/1 +CAGCAGTTTTTCTACCGGATCGATCACCGTGACGCGATGTCCACGCTCCTCCAGGAGTCCCCCTATAATTGCGATCGACATTTTTTCGTCACGGCAAATC ++ +@CCFFFBFDBHH2JJGEIJIJIJ#JBAD@.BFB5BC##A?DAAE>DCBD +@NC_003198.1-20/1 +CGACCGTACTTTCCGCCCCCGCGAAAATTACCAGCCATCTAGTGGAGATGATTGAAAAGACTATCGGCGGCCAGGATGCTTGGGCGAATAACATCGATGC ++ +?CCDDFDDHHCHHGFJAIAGJJJHICHJ9#9GHEI8#JJI??IDCDIEJJIGIF#CHF9IE?>2DI=DF#>H>G>C;#H#FDDC:D##>(DD@##, +@NC_003198.1-18/1 +TTAACCAATATAGGAATACAAGACAGACATATAAAAATCACAGATTACGCAACAACCATGAACCGCATCAGCACCACCACGTTTACCACGATCACCAATA ++ +@BCDFFFFGHDH?JII:#IFHJ@##@C?@##DDCD@DD#DD +@NC_003198.1-14/1 +AACGTTTTCTGCGTGTTGCCGATATACTCGAAGGCAATTCCAGGCAAGGGCAGGTAGCGACCGTACTTTCCGCCCCCGCGAAAGTTAGCAACCTCCTGGT ++ +?@CFFDDFDHDDHIDIGJIC+FG:3#HJ#I=B##@ICGIGDJI9EJIII@JJGDJGCDBC(DF.DHHGBDCAB#DAC#DDAE>##DDDB, +@NC_003198.1-12/1 +ACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTCGCCGATATTCTGGAAAGCAATTCCAGGCAAGGGC ++ +BCCFFFFDH3HFGADGGEJJBJJIJHEGFIJJHIG#GECDFIIJJJBB?BJD6JJJC>CHJ=GDI-DACGEGC?D@;HDA7DD>CD>FECCDD=:C@D#D +@NC_003198.1-10/1 +ACAGTGGAAATTGATTGAAAATAAAGATATCGCCAGCAGCACATGAACAAGTTTCGGAATTTGATCAATTTAAAAATTTATTGAGTTATGCCGCCAGATA ++ +@#;C#(@#C#CD8@#C +@NC_003198.1-8/1 +GGCCGGGTTCTGGCTGGCGGCGATACGGCGAGTCGATTCCGCGATACCGACGGTAGATTCGAGGTAATGGCCAACCGCCTGCAGTTTTTCTACCGGAGCG ++ +CC@7FAD#HHHHHII+AHIEJIGJEGJ:IIJGF?GCDIC/EFBAD +@NC_003198.1-4/1 +ATCGCCACCAGATGGTTGGTAATTTTCGCGGGGGCGGAAAGTACGGTCGCTACCTACGCTTGGCTGGAATTGCATTCTAGAATATCGACAGCATGCAGAA ++ +C@@FFFFF?HAHHE7BIICHJJJJDHEJEGHJJJJIIF@J?EFIHGJ@:;HJJDI#I#I#EB#B8IJH<6EAC#)#B#>D?(#@##D>(2A##<, +@NC_003198.1-2/1 +ACAACATCCATGAACCGCATCAGCACCACCACCATTACCACCATCACCATTACCACAGGTAACTGTGCGGGCCGACGCGTACAGGAAACACCGAACAGAG ++ +@@@+FFFFHFFF)JJAJIJJI@+IJGJJIJJ?GDAJ#DDED>D@CA#D9##5#C> diff -r 000000000000 -r b7b1c8bf7ae0 test-data/NC_003198.1_simulated_R2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_003198.1_simulated_R2.fastq Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,180 @@ +@NC_003198.1-90/2 +TTTCGCGGGGGCGGAAAGTACGGTCTCGACCTGCCCTTGCTTGGAATAGCTTTCCAGAATATCGGTAACAAGCGAAAACCATTCTGCATTTGACCCTGAT ++ +=@CAFDF+CHFFHHHEI,IEJJGJH#G#HIJJDI?9B??H#I3IBI*(JIDHI#HD&9DI#@HC#!E@;I!>D###H:#E#DCFD9>HADDB#A##@CAC +@NC_003198.1-88/2 +GTGATTTCTGGTCGAAAAGAAAGCTCGCACTGGCCATGTGCGGGCTTTTTTCTGTGTGTCCTGGTCGCGCCACCATGCACAGGTAGCTCTGGTAATGGTG ++ +@:BFA!C0HFDHFJCBHJ#+#:#CD##D#CC#CC3CADCC +@NC_003198.1-86/2 +TTTTTCGGACCTGCTCGCAGGACTTGCCAGCGCGGAGTCTGGATTCCCGCTTGCAAGGTTAGAATTGGTTGCCCAACAACTATGCTCGTGGATCACACTT ++ +CB1DFF!D?A8HHJFBI#JIAD@E9CI#F*JCIJ#GJ#J#@##8JFFFFE*HID;#IJ#=#!GI!FCIF?##@#).DDD##EH#:#####>(####CB#? +@NC_003198.1-84/2 +CTGCCAAGTCCTGCGAGCAGGTAAGAAAAAATACGTTCGGCATCGCTGATATTCCGCAAAGCATGCTGGCGGGCGATAGTTTTTTCTATAATCGCCATCA ++ +@?+!DFFF#EDDDD###B< +@NC_003198.1-82/2 +ATGCAGAACGTTTTCTGCGCGTTGCCGATATTCTGGAAGGCAATTCCAGGCAAGGGCAGGTAGCAACCGTAGTGTCCGCCCCCGCGAGAATTCCGAACCA ++ +@@BFFDDFFHGHHIHHDGI#HIEI>IGIGJ#0DI*DCI0JGIJ=FEJIJGHF?@IC(DBDD##HJ#>@DC#C#@#@,C@EBDCD:#D +@NC_003198.1-76/2 +AGGAGTCCCGCCATAATCGCGATCGACATTTTTTAGCCACGGCAACTCAGCGCAGCGTTGATGCTATCCGGGCACTGACCCAGCAGGCTTATACCGTGCA ++ +BC@FFDEFFHDHH)I@1IAIJHHJ3@JJEJJ)HC!FJH@CGH??I!GIHICFB#FECBBI8AJIGJ@EDDJ#95AI5IEHD9C#?#CD@#CC>CB#BDC' +@NC_003198.1-74/2 +TGTTCGACAACCATTCTGGTCCGTGAAAGCGGGAATCCCGGCTACGCGCAGGCACGTCCCGCGACCAGCTCGGAAAAACTACATTTGGCATTGATGATCT ++ +=C@F=?2D#:H<:JJ!I!##JG+H<#;)GFJID:HHFIJFJGI#GF#BGC#ID8J#HII##CGD.E##>#HD#D#5?JFF;IBAJBAEJHJDHDJCD@>;GBC!FE##DDCEC#(B?C#::HD#@CB##D' +@NC_003198.1-68/2 +TTAGCGAATTCTTGTTCGACAACCATTTTCAACCGTGCAAGCGGGAATCCCGGCTGCTCGCTGGCAAGACCTGCCAGCAGGACAGAAAAAATACGTTCGG ++ +C#?FDFF>H:HHHGIJHJJCH>GIEGJ@IIGIIJE?IEFEGD>BJJ0FJ#HEBB@IJ##FJG>GDGJ7#AEFGH#DF;5D@#D#9#' +@NC_003198.1-66/2 +TTGCCTGGAATTGCTTTCCAGAATATCGGCAACACGCAGAAAACGATCTGCATTTACTACTGGTGTACGGCCGAACTCCAACACTCGCATTGTATTTACC ++ +<@84FFFFH>G#H@I+AIIFGHJE:IEA<<:EIBHF?G1?IIAGJ!H;IAF=IHH#B#CF@F!#JFE.#FBHCEBBE#DCA?D>#BA@CD#FA##?CCCD +@NC_003198.1-64/2 +GCAAATGCAGAACGTTTTATGCGTGTTGCCGATATTCTGGAAAGCAATTACAGGCAAGGGCAGGTAGCGACCGTACCTTTCGCCCCCGCGAAACTTAACA ++ +BBCB=2DFHAFGCDII?C#JDJ<+JIJGJI?IG??IDIIBJ9J?GG#IJ#G=JJCIG=@G#FCGIGC;@6D>ACCJ#CD!DA5C@C>#ECC#:#C#D#@' +@NC_003198.1-62/2 +TCCGCCCCCGCGAAAATTACCAACCATCTGGTTGCGATGATTGAGCAAACTATCGGCGGCCAGGATCCTTTGCCGAATATCAGCGATGCCGAACATAGAC ++ +:C1DBFFDHAFAHJGJGHJ33ID#JCG?I#EJ#GFFD@J?GCGD*#BIG?HHJ;IJFC7@DG8D)F!DJHHC.@I?@=##CGDC#CBD#D#C?8#C###' +@NC_003198.1-60/2 +ACTTAGGCGGGCAGATCCTTTGACCAATAGAGGAATACAAGACAGACAAATAAAAATGACACAGTACACAAGATGGGTGACCCGCATCAGCACCACCGCC ++ +CC@BDFFF#HGHBIFI#GG#J!JDJHJGE#EDJJICII)JHIFJEJIED=D@=CHBCCA#>DDBC#C:#BD +@NC_003198.1-58/2 +ATATCAGAGATGCCGAACGTATTTTTTCTAAGCTTCTCGCAGGACTTGCTATCGCGCAGCCGGAATTCCCTCTTGTAGGGTTGCGAATGATTGTCGAACC ++ +@?C+FDF#:HFHDJ:F:JACCIGCG@AJF#@#@41?G)?I#IIDIJJJI#9#IICD#H@FHFF#HH=AID#I>F>#D##A<3B)#FC#C#C>C7??#CD! +@NC_003198.1-56/2 +GTTGGTAATTTTCGCGGGGGGGGAAAGTACAGTCGCTACCTGCCCTTGCCTGGAGTTGCTTTCCAGGATACCGGGAACATGCACAAAACGTTCTGCATCT ++ +@C@BBFDB:HDCH2IJAJCH#IIH+II@IH#FGEJJCC?GCGJAIG*JFEEF8>(@JJFIFG;####CC>#HHH#DB=C!D#B#@D<>CE#2C>>CA@#' +@NC_003198.1-54/2 +GTTTCCAGAATATCGGCAACACGCAGAAAACGTTCTGCATTTGCCATTGATGTACCGCCGAACTTCAACACTCGCAAGGTTATTACCACGTGATCTCGTG ++ +#?CFAADFGEHHB+?JHJHHJI+6HG0J<9E=ED#IIGH@JC#>F@###GF#AI;JBBJFEBIJHIGCBAF@FFD9#D<57!;CDBC#EBC@EB@C>##D +@NC_003198.1-52/2 +CGGCTGCGCGCTGGCATGTCCTGCGAGCAGGTCAGAAAGGATACGTTCAGCATCGCTGAGATTAGCCAAAGCGTCCTTGCCGCGGATAGGTGATTACAAC ++ +CCC4#)DDFEAHH@I#+FGIEFCIIJHEFIGCGFGGG*##FBI*GG6H!HBC0I(IHI>+DID#<#DH;EHF!DHC8#58EDD#ADD#C#>#!E###D#9 +@NC_003198.1-50/2 +GGCTGACGCGTACCGGAACCACATTCAATAGCCCGCACCTTAACAGTGCGTGATTATTTGTCGACCAGAGACCACGTGGTAACAACCATGCCAGTGATGA ++ +@@?DFF<;DHHFH#J+G.#I4?J##+AG#GBFJH)IC@JI#I?HI?IACI!F#JG##JF#CJECDF#IJ#D#FHDC#BFC6E#:DD>DCED#D>B<#C#' +@NC_003198.1-48/2 +ACGCGCCTCCAGGAGTCCCGCGATAATCGCGCTCGACATTTTTTCTCCACGGCAAATCAGCGCGGAGTTGATGCTATCCGGGCATTGACCCATCAGGCTT ++ +=CCD4DDFBEHG?JE#+CG9?#1J2H:IJHC#HBGJI#I#FIHIG!IGA>GFAJDEFG,DAEE#I#IE;EFF?@BG?3BDB89D#DIHHE#A#IIDJHECJH#IHFDJI#JCGGHHIIBG(=@EF?8F#H#BFJBD>DAFD@#@#E#DCAADDD??#C#' +@NC_003198.1-44/2 +TCGCGACCTGCCATTGCATGGAATTGCTTTCCAGTATATCGGCAGCACGCAGAGAACTTTCTGCACTTGCGAGTGTTGTACAGCCGAACGTCAACACTCG ++ +CBCF#F?FHH8H#EBGE#J#CJGJJEJB##JFBA#E#?##IFBCC#B##>DC@#>:@ID?J!G9JGJ*EJJJGG'IGGHE#D=###E@HJEDI#GHFE!)CF##B:##FDC##F#8!CCCB#5@: +@NC_003198.1-40/2 +CATTCGAATGTCGAAGGTCGGAGGTACATCAGTGGCAAATGCAGAATGGTTTCTGCATATTGCCTATATCCAGGAAAGCAATACCAGGGTAGGGCACATA ++ +B?C!FF=#HCH#HHH<#JICD!GIJIGEHI#DJ#EJJGJHJJHID?#D#IGDI=3H#H#GC##@#D9J##D##3FABFFCCD#@F3#H!#C>:CC@##>: +@NC_003198.1-38/2 +GTGATCAATTTAAAAATTTAGTGACTTAGGCGGGCAGATACTTTATCCAATATAGGAGTACAAGACAGACAAATAAAAATAACAGAGTAAACAACGGTCA ++ +BBB4D=D:HEH#DHID,CJH!HJI+AJ>GJH:G?C*FJAB99CGI#JJDJCCDD4GI#IF?0?DDD#5C##D#A9A###>D +@NC_003198.1-36/2 +TGGTTGTTACCTCGTGATCTCTGGTCGAAAAAAAAGCCCGCACTGCTCATGAGCGGTCTTTTTTCTGTGTTTCCTGTACGCGTCCGCAAGCATCTTTCCC ++ +B?BDACED2?;DH)JDJG0HGHAIJJGIE@H;GAIJID@JGF8GG#JBG#I#G9ID#C?EHJH=5D2IICFCII#B#HECHDDB#B##!:CC#>#?E#;D +@NC_003198.1-34/2 +AAATATATCGCCAACAGCACATGAACAAGTTTCGGAAGGTGATCAACTTAAAAATTTAAAGACTTAGGCGGGCAGATACTTTAACCAATATAGGGATACA ++ ++C+DFC;FH+#1G#HAJJIDH#JHJCJGBFDCFFJBJ#JH*JII#B!J'H@GH@?GH>##HDB8J=DH@CBCC57CC8CDGF@C(D5E#>EDD:#DCAC' +@NC_003198.1-32/2 +ATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAATCAATTCCAAGCAGGGGCAGGTAGCGAGCGTACTTTCCACTCCCGCGAAAGACACCAACCA ++ +BC@D=D=DHEHGGJHI+J+GJDJICJCI?I*#GIHJ9JD!??GJ08G>#HHI#GFCFJ#IG;I>JD##?D#DGEA#H!9!D#EDD@#3;###@D:>>@AC +@NC_003198.1-30/2 +AGGCTGATACCATGCAAAACCTGTTAGATCTGAGCGAATTCTTGTTCGACAACCATTTTCACGCGTGCAAGCGGGAATCCCGGCTGCTCGATGACAAGCC ++ +@?B#BFFA4EAHHGJCJIIH#>G#3!>EGI04#J9FHJIIBJFJFE@?4#I8?D?DDEJJA##BI@HD>D>DCFD#8H=A#/C;CGD#AC#DC##BB##D +@NC_003198.1-28/2 +CACGCGCCTCCAGGTGTCCCGCCATGATAGGGATCGAACTATTTTCGCCACGGCCAATCAGCCCGGCGTTGATGCTATACGGGTACTGACCCAGGAGGCC ++ +B=1DFFFED2DD<##@AD@' +@NC_003198.1-26/2 +TTTTTGCGACCATAGATCACGAGGTAACAACCATGCGAGTGTTGAAGTTCGCCGGTACATCAGTGGCAAATACAGAACGTTTCCTGCGTGTTGCCAATAT ++ +?BCAF)F2DGH<#JICG@JJH#0?AG#@JI/AFJI@#GDD0BG;:?GIFCG#EICICD#B/4GG(BJ3J@D#E(?IAGDH;@#D6ACCFC##DDD##D#' +@NC_003198.1-24/2 +GAAACACAGAAAAAAGCCCGCACCTGAGCAATGCGGGCTTTTTTTTCGACCAAAGATCACGAGGTAAGAACCATCCGAGTATTGTAGTTCGGCGGTACCT ++ +@BBDBFF+HH?HDGIJ0CDC##@ +@NC_003198.1-22/2 +CTATCGGCGGCCAGGATGCTTTGCCGAATATCAGCGGCGCCGAACGTAATTAATCTGACCTGATCGCAGGACCTGCTAGTCCGTAGTCGGGATTCCCGCA ++ +B?@4DFDFA?CDH@JJIGJIJAHEIHJIDEHC!DFBDCDD#3>BD' +@NC_003198.1-20/2 +AATCGCGATAGACATGCTTTCGCCACGGCAAATCAGCGCCAGGTTGATGCTATGCGGAGACTGACCCAGCAGGTTGATACCATGCAAAACATCTTTGTTC ++ ++@BFDFFFH#C++C>##JIBIIC#J<#FC)GDF9:J*JI!#!##B@#C;IGJG##G:##F3FJFH'DJ#9I#9#9C>?IC(CCDCC?EC@AD#@BDC#DD +@NC_003198.1-18/2 +CCCTTGCATGGAATTGCTTTCGAGGATATCGGCAACACGGAGAAAACGTTTTGCATTTGCCTCTGATGTACCGCCGAACGTCAACACTCTCATGGTTGGT ++ +?@CFD>C#HHFHHGFHFJJH##JJ#JFIJJD?@*#JCCJ#@FJ?JBJD:I!;II1JGGHFG#IJ=JIE;IED@DF?HDE#CD@@CC?:4#DD:DDCCD#' +@NC_003198.1-16/2 +TCGTGCAAGCGGGAATCTCGGCTGCGCGCTGGCAAGTCCTGCGTGCCGTTCAGTAAAAATCCGTTCGGCATCGCTGATATGCGCCAAAGCATCCTGGGAG ++ +#@@FF=DDBCGGHHI#A#GC3A?I#IHJIGJIJ?GHF##ICGB#:J#F#GH-I#JJIGJE#H@##IFCIE5;=C>CCB#C#ED#FCFD9D6?CC@C@##> +@NC_003198.1-14/2 +CGTTGATGCTAACCGGCCGCTGACCGAGCAGGCGGATACCATGCGAAGCTAGTTTGATCTGAGCGCATTCTTGTTAGATAACCATTTTCCCCCGTGTACG ++ +?B@DF?CDFH2#:H#J#I!JHGJJG!IEJCG?**JIC?BJ#EJ2####H##=GJ8)JJGI@##D=#=E>DC>#BC#BC##D)@3#C?#C#!###@?#D#@ +@NC_003198.1-12/2 +TCTTGTTCGACACCCATTTTCACCCGTGCAAGCGGGAATCCCGGCGGCGCGCTGGCAAGTCCTGCGAGCAGGCCATAAAAAATATGTTCTGCATCGGTGA ++ +@BC++DDBDEHG#GJI<IDFE(C#A@#CH>E#D#C#FDC?#>ACDFD#D>D +@NC_003198.1-10/2 +CGCATGGTTGTTACCTCGTGTTCTCTGGTCGACAAAAAAGCCCGCACTGTTCAGGTGAGGGCTTTTTTGGGTGTATCCTGTATACGTCAGCCCGCAACGT ++ +@@CBDF?FHF>H=7GDF##@D#EH-BDFEE!D>!A#B>?#D' +@NC_003198.1-6/2 +TCGCCGGCAGCACATGAACAAGTTTCCGCATCTGTTCCATTAAAAAATTTATAGACTTAGGCGGGCAGATACTTCAACGCTTAGACGAATACAAGCCTCG ++ +CCC+D##FAF#A##' +@NC_003198.1-4/2 +AACCGCATCAGCACCACCACCATTACCAACATCTCCATTACCCCAGGTAACGGTGCAGGCTGACGCGTACAGGAAACACAGACACAACGCCGCACCTCTA ++ +@+BF4FFFHAD<I#GI)C=F:###9A@DDDD##' +@NC_003198.1-2/2 +ATTGTTTTTTCAATCATCGCCACCAGATGGTTGGTCATTTTCGCGGGGGCGCAAACTACGGTAGCTACCTTCCCTTGCCTGGAACCGATTTCCAGTAAAT ++ +C#!+D+*FJ#EJ9=8#FGG##CJFI.#ACFBH=D!E?55>;D3BHABA##C#BAC?CDD#?#EC diff -r 000000000000 -r b7b1c8bf7ae0 test-data/NC_003198.1_simulated_bracken_report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_003198.1_simulated_bracken_report.txt Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,2 @@ +name taxonomy_id taxonomy_lvl kraken_assigned_reads added_reads new_est_reads fraction_total_reads +Salmonella enterica 28901 S 40 2 42 1.00000 diff -r 000000000000 -r b7b1c8bf7ae0 test-data/NC_003198.1_simulated_kraken_report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_003198.1_simulated_kraken_report.txt Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,13 @@ + 6.67 3 3 U 0 unclassified + 93.33 42 0 R 1 root + 93.33 42 0 R1 131567 cellular organisms + 93.33 42 0 D 2 Bacteria + 93.33 42 0 P 1224 Proteobacteria + 93.33 42 0 C 1236 Gammaproteobacteria + 93.33 42 0 O 91347 Enterobacterales + 93.33 42 2 F 543 Enterobacteriaceae + 88.89 40 0 G 590 Salmonella + 88.89 40 0 S 28901 Salmonella enterica + 88.89 40 0 S1 59201 Salmonella enterica subsp. enterica + 88.89 40 0 S2 90370 Salmonella enterica subsp. enterica serovar Typhi + 88.89 40 40 S3 220341 Salmonella enterica subsp. enterica serovar Typhi str. CT18 diff -r 000000000000 -r b7b1c8bf7ae0 test-data/NC_011750.1_1kb.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_011750.1_1kb.fasta Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,14 @@ +>NC_011750.1 Escherichia coli IAI39 chromosome, complete genome +GCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCT +TCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAAT +ATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCA +TTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGC +CCGCACCTGACAGTGCGGGCTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGT +TCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAG +GCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAA +AAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTCTGA +CGGGACTCGCCGCTGCCCAACCGGGATTCCCGCTGGCGCAACTGAAAACTTTCGTCGATCAGGAATTTGC +CCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTG +ATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTA +CCGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGA +GTCCACCCGCCGTATTGCGGCAAGTCGTATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCGCC diff -r 000000000000 -r b7b1c8bf7ae0 test-data/NC_011750.1_simulated_R1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_011750.1_simulated_R1.fastq Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,180 @@ +@NC_011750.1-90/1 +TAAAATTTTATTGACTTAGGTCACTAAATACTTTAAGCAATATAGGCATAGCGCATAGACAGATAAAAATTATAGAGTGCACCACATCCATGTAACCCAT ++ +CB@D#FFDFBHFDJHJJIEHJJIFIJGJFIJ#?EG?#DGFGCII0?FJJIDIGJ*#GEIJ#IJ?)BC5EHD##>F8A;#@FA#A>;BDD>DD#C#8#@?C +@NC_011750.1-88/1 +TGGCGCAACTGAAAACTATCGTCGATCAGGAATTCGCCCAAATAAAACATATCCTGCATGGCACTAGTTTGTTGGGGCAGTGCCCGGATAGCAGCAACGC ++ +CC1FFFF=D2D+HGIHJ#3JFIIAIIAIGJJFEJ#JGJJIJ?IIGC@BDB#HIHIB;FA5D#DA#D#FCDC +@NC_011750.1-86/1 +CTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCAAGCGAGTGTTGACGTTCGGCGGTACATCGGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGA ++ +5C>FAFAFHDCA=C@#D<@DC#DDD>D:DDA#D?ED, +@NC_011750.1-84/1 +GAAAACGTTCTGCATTTGCCACTGATGTACCACCGAACTTCAACACTCGCCTGGTAGTTACCTCGTTACCGTTGGTCGAAAAAAAAGGCCGCACTGTCAG ++ +@C=DFDFFFHGDCGEIIIJD?#JAIIDBHJ?#JEGGIBFJIJ=J>FGIJD##DI?!EE=JBBJ#FBD=DI#?E;CECDDCB53DD +@NC_011750.1-82/1 +TGCTTTACCCAATATCAGCGATGCCGCACGTATTTTTGCCGAACTTCCGACGTGACTCGCCGCTGCCCAACCGGGCTTCCGGCTGGCGCAACTGAATACT ++ +@@?A#FDDHGHF<>JJ4GAIIICCD0###EEIIHIIJ#JHGJJHJIB#'FHH#IJCJJCJ8GEG7??-?>EF(C?#;C7?#DH#CDABDDAD?DBA#DC@ +@NC_011750.1-80/1 +TGGCGCAACTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTTGTTTGGTGGGCCAGTACCTGGATAGCATCTACGC ++ +@C=DFEFFDHHHH#CHEEIICIJHJJJJ#JGGGHJFJIJBED=?DEIHH>BJI#CGIBEI#I>DC#HBGED)HE?:##ED5#CE#EAE2EC5DDC##BAC +@NC_011750.1-78/1 +GTCCCGTCAGAAGTTCGGCAAAAATACGTTCGGCATTGCTGACATTGGGTAAAGCATCCTGGCTGCTTGTGGTTTGTTCAATCATCTCCACCATGTGAAT ++ +@@CFFFFFFHHH#JJJIJJHJHFAJJI#J#I:HIJG#JBGH@#H3JEII@?IIFIHBFH9EC@#J=D##FCEIC;#@CD4EFECAD#D3DDC8#C+>##@ +@NC_011750.1-76/1 +GCAGAACTTCAACACTCGCATGGTTGTTAACTCGTTACCTTTGGTCGAAATAAGAGCCCGCACTGTAGGGTGCGGGCTTTTTTCTGTGTTTCCTGTACGC ++ +C?!DD#;FC7FHAHI2JJEI=HJ?IIJJI#HICHJGHJ8IJGI;JD@H*FB@J#CGI@EBA#JEEG##E#GDCCE?DHJFA<#>>AD#C>?E>8AD#ADB +@NC_011750.1-74/1 +AGAACGTTTTCTGCGTGTTGCCGATATTCTGCAAAGTAATGCCGGGCAGGGGGAGGTGGGCATCGTGCTCCCTGCCCCCGCGATAATCACCATCCACCTG ++ +??CFFDF1HFH#E#FC(E#C;CD:#,>#CDDCC#B#?, +@NC_011750.1-70/1 +ATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGAAGCTTCTGCACTGGTTCCCTTACGCGAGTAAAGTAAAATGTTATTGGCGTAGTTCTCAAA ++ +CCCFFBFFHA@HCJIHJGGGBJJJJJIJFA1>J#IHBAD#FG#HAH#@#FH@BC1##IJD!#FH#7@?AD@E!A>:I@B#D#;#??#A##D##@D#B#?D +@NC_011750.1-68/1 +CCGCTAATGGTTTTTTCAATCACCGCCACCAGGTGGTTGGTGATTTTGGTGGGGGCAGAGAGGACGGCGGCCACCCGCCCCTACCTGGCATGGCTTTCCA ++ +@CCDFFEDHDHH=#EIIJIJHH#JJIB:EGJIFI096HGJIEFJFIGJE#JIGJIBHJDJCBFGJGH#;?HID;E#F>I=@F#EDD5BDC@#D#DDCCDD +@NC_011750.1-66/1 +CTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTCGACCAAAGGTGACGAGGTAACAACCATGAGAGTGTTGAAGT ++ +@@@FF+FFHFHHHIJI?/IJECGEJHHB;FC(EHCJD?5;F#EDEF=EH#D?@E>C#DF#>CB5#D??A +@NC_011750.1-64/1 +AAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACGATTACCACCACCATCACCAGTACCACAGGTAACGGTGTGTGGTGACGCGTTTTG ++ +?@CDDDFADH?HHJG#JBGJ@BJJAJHEGJIIFGJIIIJJBJIJI##IAEHDGCAIBH#HGFAJJ#GFHDD#D;#;=#GCBCE#D#D#DDDA>#@<###, +@NC_011750.1-62/1 +TCAACACTCGCATGGTTGTTGCCTCGTTACCTTTGGTCGAAAAAAAAGCCCGGACTGTCAGGTGCGGGCTTCTTTCTGTGTTTCCTGTACGTGTCACTCC ++ +C@+FFFFDC#D=>#?E,;DC5D#D,BE##AIF>!I7#GJE#F#HD#.>@#E#A;@D>DDB#C#@C#B +@NC_011750.1-58/1 +CTCAGTAATATCGACGGTAGATTCGAGGTAATGCCCCACTGCGACCAGTTTTTCGACAGTATCGATAACGGTAACGTTGTGACCGCGCGCTTTTAATACG ++ +@@@F8#FFHDHDH#GGJJIHHECIJFIJ?@JGICJICJFJ:##J#F?JEIFIJHCIJ#H#;DEHGDCI@GFCHF>G8BFC2>A#EDEDDCED#@CCD#C, +@NC_011750.1-56/1 +GTTTTTCGACCGGATCGATAACGGTAACGTTGTGACCGGGCGCTTCTAATACGCCGGCCATAATGGCGGTCGACATTTGCTCGCCACGGCAAATCAGGGC ++ +@@CAFDFBCHFHDEFH?EIJIJJJI#JJ>JIHBGIJIG!JAFIGI#JIBGGJGDH3DEIF7GE#DG-CFHH#5F.JFC:DHB=FFCABDDCD?#DDD#:AD, +@NC_011750.1-50/1 +TTTCATTCTGACTGCAACGGGCAATATGTCTCTGTTTGGATTAAACAAAGAGTGTCTGATAACAGCTTCGGAACTGGTTACCTGCCGTGGGTCAGTTAAA ++ +CCCF;2FFGHHHHJGJHJH?GFEGIDFJI9JIJGH#GGJJBGI>D#9I#HJEJ:IED/>J>#D;CJ>IB#FDCBFEAHDCCCEBDCD#D##E#B#AA>>D +@NC_011750.1-48/1 +CACGGCAAATCAGCACAGCGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGACCTGTGTTATTTGGGCATACTCCTGATCGACTAA ++ ++1@DFDFF+?HHG<#IHJBJJIJJB>JBGHJGHAGFAD#5#C#@3@0C#B8C#68 +@NC_011750.1-46/1 +CCACGGCAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCCATCAAACTAATGCCATGCAGGACATGTTTAATTTGGGCGAGTTCCTGAGAGACGA ++ +@@@FDF?DH?FHCJJ:EGH:GJJJJ:IEDIA<=CGH#BE>5G=(D#:H6D8D#;#;@FDDD###@CDB, +@NC_011750.1-44/1 +TTGCCGAACTTCTGACGGGACTCGCCGCTGCCCAACCGGGATTCCCGCTGGCGCAGCTGAAAACTCTCGTCGCTCAGTAATTTGCCCGAATAAAACATGT ++ +BC@DFF##>C9#>CF7@#DF##@CA>AAB>BCEC +@NC_011750.1-42/1 +CCACGGCAAAACAGCGCAGCGTTGATGCTATCCGCGCACTGCCCCAGCGAACTAATGCCATGTAGAACATGTTTTATTTGGGCAAATTCCTGATCGACGA ++ +@C@FFFBFHH#BHIIDIE9CIIIIIJ?FEC1IJI#IGC@J8A8JJI#E#=HII@C?AA@GCCC5:DBAEFE?CB@:CAB9D +@NC_011750.1-40/1 +TGGCCACCGTCCTCTCTGCCCCCGCCATAATCACCAACCACCTGGTGGCGAAGATTGAAAAAACCATTAGCCGGCAGGATGCTTAAGGCAATAACAGCGA ++ +C?CDFADFADH:GCJH;IHJ>JICHGJ#J9DIDBJJFBJHGJHJ#FF;AC8, +@NC_011750.1-38/1 +GGTTACCTGCCGTGATTAAATTAAAATATTATTGACTTAGGTCACTAAAGACTTTTACCAATATAGGCATAGCGTACCGCAAGACAAAAATTACAGCATA ++ +;@CFFFF23HFFCJG#DG?IGHJJI:H#JJAJ?7EI#JJ3I>GJJJJ9B#IHFHD#IJ#EH@AIBEFBDCC=DJ#AE#D##@CC##CDDC:CDBB5##CC +@NC_011750.1-36/1 +GAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGGACGTATTTTTGCCGAACTGCTCATGGGGCTAGCTGCTGCCCAACCTGGAT ++ +@C?FFF?FFHFHHGGGGHJIBJIJJH)?J:GHIIDFIGDJJIGJJJ?ED#JGJGFIJGJJGBCBJFFD#JD#D#GBG#H<#ED#A=D@DD=B#CD#>AC> +@NC_011750.1-34/1 +TTCTCGCCACGGCAAATCAGCGCAGCGTTGATGGTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGATATGTTTTATTTGGGCAAACGCCTGAT ++ +@@@?F+DFHHA8+JJJIJJJGJI2EJJJI#I#H#?F#GDIFGIG?G=JCJIIGBII:IIHIEH?DJEDCI#CEAJJJJJIIGIJCJG?HHJIFAH?EJCJ?G0JIJGGGF+7JHI=EBB#H;G;B@AD@DDC=DAFD#B:CDC#D@ +@NC_011750.1-30/1 +TGCCCCACTGCCAGCAGTTTTTCGACCGGATCGATAACGGTAACGTTGTGACCGCGCGCTTCTAATACGCCGGCCATAATGGCGCTCGACATTTTATCGC ++ +@C=FFFFFFGHBDIIJJGI?IG,JFCHJJ#JFIJ;IHIHJ@E*FJHEIJJJGBJ>G4GE#G@D@?;<(DC#E#(CC:#DC@#19CA +@NC_011750.1-28/1 +AAAAAAGAGTGTCCGATAGCAGCTTCTGAACTGGTTACCTGCCGCGAGTAAATTAAAATTTAATTGACTTAGGTCACTTAATACTTTAACCCATATAGGC ++ +@@CAFDFFHHFH<#FIAJAGFEJ=IJJIJJJFEIHI7#IHJJ3J#EG=AIGGJDHEAE74A'DFHJAIJJCGIDEHH>#;HCDEFA?:DA?#CDC?D#:C +@NC_011750.1-26/1 +AATGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGACGAAGGCGGCCACCGTCCTCTCTGCCACCTCCAAAATATCCAACCACCCCGT ++ +=B#FDFAFDHGGBJF@JGIJIJJIHHIIGI0H<0#GIAJJIFFJCI###I!GEJ#JDGGI=GAAGAGCDFB;#F#?B#ACEA#:>##CDDAE>C9###AB +@NC_011750.1-24/1 +CGGTGGCCACCTGCCCCTGCCTGGCATTGCTTTCCAGAATTTCGGTAACACGCAGAAAACGTACTGCATTTGCCACTGATGTACCGCCTAACTTCACCCC ++ +CC?FFFFFH3HHHJJJJJHCA2#;#DD:DC<5(#C3CD0ADCD +@NC_011750.1-20/1 +TAATGGCGATCGACATTTTCTCGCCACGGCAAATCCGAGCAGCGTTGATGCTATCGGGGTACTGCCCCAACAAACTAATGCCATGCAGCTCATGATTAAT ++ +?@CAFFFFFHHDHJJJ@EJDG@JIHAF@#J?CFJG#I#J#JIBIH'HIDFJIHJ=##F=#DC@H=FHJFEJD><@F?GDD@C@FBCFB##B@AD#C@#C, +@NC_011750.1-18/1 +CGATGCCGAACGTATTTTTGACGAACTTCTGACGGGACTCCCCGCTGCCCCACCGGGATTCCCGCTGCCGCAACTAAAAACTATCGACGATCAGGAAGTT ++ +@@CDFFFF?GFH:F#GC@F@;@#CBIFC##D>D#C@B#DD>ABA#B, +@NC_011750.1-16/1 +GCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCCACAACCACCTGGTGGCGAGGATTGAAAAAACCATTAACGGCCAGGACGCAT ++ +BCCFFFDFFDAH>GIIICHGHIIDJEJJDJFJJJEIEHGIJICJJJHH##JGHGIFIFE#BIJ7G=G#G7EDFICCE#?F#>@DD#1CCCCDAC##DD#B +@NC_011750.1-14/1 +GAAACACAGAAAAAAGCCCGCACCTGACAGTTCGGGCTTTTTTTTCGACCGAACGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGTCGGTACCAC ++ +@@@DDDAFHB+HF@JFIJH:IIJ?HH#JIHA#JHDCJG#II7)JBJ@JII#EA#GIEFG8JHFED#DC:DDD##C +@NC_011750.1-12/1 +CTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTTCCATGAGTATATTAAAATTTTATTGACATTTGTCCCTAACTACTTCA ++ +;C>F-FFFDHHHHGJG?JJJJEJJJJJDAIGDGIJGGJ4IIJAID0#FJJ;G#ID#G8@IIH#@A#GGIHBDED:#D;CC#D##BB##C@D@#DC?D?#D +@NC_011750.1-10/1 +TTCGAGGTAATGCCCCACTGCCAGCAGTTTTTCGACCGGATCGATAACGGTAACGTTGTTACCGCGCGCTTCTAATACGCCGGCCATCATAGCGATCGAC ++ +CB5=HI#)DFGAH@:IHJIJ3E>DF?#BDFDE9E#DD#E7CCBAEC> +@NC_011750.1-8/1 +TTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGTGCACAGACAGATCAAAATTACAGAGTACACAACACCCATGAAACGCATTATCACCACC ++ +@CCFDFDEGHHHFFJI77CJ:HIJJJGIJI?GH3JJ)DBGJ#A=D8JF?#DBGJ.BIFJG(.#F=#C?AEF7DJ?H#5@>:DCDDDIB+E#;#3D:93BC +@NC_011750.1-6/1 +ACTTGCCGCAATACGGCGGGTGGACTCAGCAATATCGACGGTAGATTCGAGGTAATGCCCCACTGCCAGAAGTTTTTCGATCGGATCGATAACGGTAACG ++ +BC@FF=FFHHDHHGDAJ>GIIIGGJGAJI?I@J)II?GFJ?IIIJJJJJCDHIHJG#0FG@#EHFCDDBD#E=DB8AC>E4C##C>B>D@ +@NC_011750.1-4/1 +TGCCACTGATGTACCACCGCACTTCAACACTCGCATGGTTGTTACCTCGTTACCTTTGGTCGGAAAACAAGCCAGCTCTGTCAGGTGCGGGCTTGTTTCT ++ +CC?FFDFFDF=HDI+#EJ>#IJH?JFDFJGDIDGE?JJI9@JJGGJGIJHIGE9H/EJDCCH#F8AG#7C4A@#GD#@BGH2B@>#BD#E#?C##D@CDC +@NC_011750.1-2/1 +CCTGCCTGCCATTGCTTTCCAGAATATCGGTAACACGCAGAAAACGTTCTGCATTTGCCAGTGATGTACCGCCGAACTTCAACGCTCACATGGTTGTTAC ++ +@@CFF8FF#HHAHH7@JIBG@JIHJF2BFJ#IDIB@IIIIB@J;IJCGHGIIEB>/GABJ#BFBJHDED6@F@8H#(:BDDCAD>, diff -r 000000000000 -r b7b1c8bf7ae0 test-data/NC_011750.1_simulated_R2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_011750.1_simulated_R2.fastq Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,180 @@ +@NC_011750.1-90/2 +ATCGGCAACACGCAGAAAACGTGCTGCGTTTGCCACTGTTGTACCGCCAAACTTCAACACTCGCTTGGTTGTTACCTCGTTACCGTTGGTCCAAAAAAAA ++ +?CCB=FFFHH2HD#CB##5@##5!AFDCE##D +@NC_011750.1-88/2 +CAGCACCATGTGATCAGCCGGGATACGGCTTGCCGCAATACGGCGGGTGGACTAAGCTAGATACACGGTAGATTTGAGGTAAAGCCCCAATGCCATCAGT ++ +@@@ADFF,FFHDJIABCB@9=A!HCH#D#C?##G@CJDIG);###?A?DDC##CCA:D!?(5@>#DDF: +@NC_011750.1-86/2 +ACGAAAGTTTTCAGTTGCGCCAGCGGGAATCCCGGTTGGGCAGCGGCGAGTCCCCTCAGAAGTTCGGCAAAAATACGTTAGGGATCGAGGATATCGGAAA ++ +@1CFD?3CID;8#GEF@;=D@E#@@ABDFD(D' +@NC_011750.1-82/2 +TCGAGGTAATGCCCCCCTGCCAGCAGTTTTTCGACCGGATCAATAAGGGTAACGTTGTGACCGCGCGCTTCTATTACGCCGGCCATAGTCGCGATCGACA ++ +:@?:FDD:J>)GFEH5>C7#DD>DB6>9CHHFA#C#CA@CDC:@3' +@NC_011750.1-80/2 +ATCAGCCTGAATACGACTTGCGGCGATTCGGCGGGTTGACTCAGCGATATCGTCGTTGCATTCGATTTAATGCCCCACTGCCAGGAGTTTTACGTCCGGA ++ +=#!###C' +@NC_011750.1-78/2 +CAGTGCGGGCTTTTTATTCGACCAACGGTAACGAGGTAACAACCATGCGAGAGTTGAAGTTCGGCGGTACATCAGTGGCACATTAAGAACGTTTTCAGCG ++ +CB;F=CFFHHHHHIC#EGIHCHAHI#J4A1H@JI<19:I3JHJGA?GHIB;##FHIGFJJHG)FCBHEDDGC5F#C#D4E#BH##CFC5EA#BCC##>CC +@NC_011750.1-76/2 +TAGCAGCGTCTGAACTGGTTACATGCCGTGAGTAAATTAAATAGCTTTTGAGTTAGGTCACTGAACACTTTAAGCAAGATAGGGATAGAGCAGATAGAGT ++ +BB?4=FD#HGHDHJI2FG:)JG#?JH+I+#FIJIJ#IG*H1##!#I#D;?D#IGBG7EDAFJ#CF#D@FE#HE#HED#)IADC!7EB###D#A#! +@NC_011750.1-74/2 +ATTGCCCCAACAAACTAATGCCATGCAGGACATGTTTGATTTGGGCAAATACCTGATCGCCGGAAGTGTTTAGTTGAGCCAGCGTGAATCCCGTATGGGC ++ +C#BAF#DFF3GFBJG#IJJH@JCEJAJG?JJ0JGGHH#@1:JIFI9GF#F#ADDICHHJ!GI#EBF:#FD#IAGB###C#BDBH#5>EE:EB###AC>A? +@NC_011750.1-72/2 +ACATTATCTCGCCACAGCAAATCAGCGCAGCGTTGATGCTATGGGGGCACTGCCCGAACAAACTACTGCCATACAGGACATGTTTTAATTGGGCAAATGC ++ +?C=DF!FFGHHHDJA#>B@D#5 +@NC_011750.1-70/2 +CTCGTTCCCTTGGGTCGAAAAAAAAACCCGCACTGTCAGGTGCGGGCTTTTTTCTGTATTTCCTATACGCTTGAGCCCGCACCATTACCTGTGCTAATGA ++ +BBBF4F#;CF<#FF)JI,BJ,9+:H#C?(#D>C#>' +@NC_011750.1-68/2 +CACCTTCACCATTACCACAGCTAACGGTGCGGGCTGACGCGTACTTGAAAAACGGAAAAAAGCCCGTACCGGACAGTGCGGGCTTTTTTTTCGACTAGAG ++ +CCCD+FFFHH?BFA;?D###C' +@NC_011750.1-66/2 +ATACGTTCGGCATCGCTGATATTGGGTATATCATCATGGACGCTGATGGTTGTTTCAATCACCGCGACCATGTGGATTGTGATTTTGGAGGGGGTAGAGA ++ +@::4FD#FFH>H+J+J@IJ+I1FEIIHG+##G3:I(HJJ#I9JI#JIBHHCAIJIFGC#HD#AF=#GIJF!DJHA#F#ACEFEDDC5@#9#B>B#CC#BC +@NC_011750.1-64/2 +TGATTTTGGCGGTGGCAGAGAGGACGATGACCACCTGCCCCTGCCTGGCATTGGTTTCCCGAATTGCGGCAAGAGGCAGAAAATGTTGTAATTTTGCTAC ++ +BB:?F=D;AFHH#GIJIGJGAIJHJE!)G#1CH@IGF@IIIDEJJ-IGHI#IF#FDDFE#FGCJEICG8J#D9HFF2JCGECDHC=H=AG=#?C#F=A@C?BHC+B#?AC#!#AC>D@C##' +@NC_011750.1-60/2 +GTTACCTCGTTAGCTTTGGTCGAAAAAAAAGCCCGCACTGACAAGTGCGGGCTGTTTTCTGTGTTTCATGGACGCGAGAGCCCCCCCCGTGACCTGTGGT ++ +BC@DFDDF2H+F###D>FCB#D##CA5#C#D>C@#' +@NC_011750.1-56/2 +CCATTAGCGGCCAAGAAGCTTTAACCAATATCAGCGATGCCGAACGTATTTTAGCCCTACTTCTGAAGGGACTCGTCGCTGACACACCTGGATGGCCGCT ++ +@CC#+FCAFCHHH!EI#?#GJJ0#H9J2ECIJ?IJCF=GJG>GE>J9?9=G##J.I##JDDGBHC?#IDEG#HAC#@E@C##D##FE##DCAA##E<9DE +@NC_011750.1-54/2 +GTTTTTTAAATCCTCGCCACCAGGTGGTTGGTGATTTTGGCGGGGGCAGAGAGGGCGGTGGCCACCTGCCCCTGCCTGGAACGGCTTTCCAGAATATCGG ++ +1@+F4AD#AAF##HJJIGJ@DD#?##C@FCC#D@#' +@NC_011750.1-50/2 +GAAAAAAAAGCCCGCACTGTCTGGTTATGGTTTTTTTCTGTGTTTCCTCGACGCGTCAGCCCGCACGGTTACCTGAGGTAATGGTGTTGGTCGTGGTTAC ++ +@=@FDDF2DFHH+GEJ2AJJD!JFG#!)FE#JGHJ>#ICG?JDBFI*G##DC#CJGDJIJ@IIJDG#DCD#FCC#!>9C@>#D@BD##CDE#CDD#A#D' +@NC_011750.1-48/2 +TGCCAGGCAGGGGCAGGTGGCCACGGTCCTGTCTGCCCCCGCCAAACTCACCAACCGCCTGATGGCGATGAGTGAATAAACCATTATTGACTAGCACGCT ++ +BC@4DACDHHFF2+IC:?FHFJI,!CEHGI!DGEG)IJHDG#JI2G#BIEI=AHCB#I#FE#J#CD86BHD#ICE##EAI:=3C#C##@#C##B#@###HC#'JBJIE@GGICIIJIAG;HH#;>#ID#J3C#?@@-9#CEC?;@#:#B#@8DBB#C +@NC_011750.1-44/2 +AATATCGACGGTAGAGTCGATGTACTGCCCCACTGCCAGCAGTTTTTCGACCGGATCGATAAATGTATCGTTGTGACCGCGCGCTTCTAGTACGCCGGAC ++ +CB1FFCFFFHFDD8>E3D#D +@NC_011750.1-42/2 +CAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGACAATATCACCAACTACCTGGTGGCGAAGATTGAAAAAACCATTAACGACCCGGATGCTTTG ++ +#C@FDD?FH:FFHIIF2;E+3III<#EIHIHHHJD/GH#GIG#E4IJAJJJ#FFGD#H#EIE@BEFDCDJCH@D!CB#FD#EDDBB8B>>' +@NC_011750.1-40/2 +TGGCGATCGACATTGTCTCACCCGGGCAAAGCAGCGCAGCCTTGTTGCTATCCGGGCACTGCTCTAACACCCTAATACGATGCCGGAACTGTTTAATTCG ++ +8C?=FADDHHH#DD#E:,E#E:#)CEEJ8I#@GBGFH0JD*HDF!EJ0G?4JD8#IGEHI;H#I#F=GH##JFCBF!>#CC#B#?CE##CD;?D#AB@#> +@NC_011750.1-38/2 +TCTGCATTTGCCACTAATGTATCGCCGAACTTCATAACCCGCATGGTTGTTACCTTGATACCTTTGGTCGGAAGAAAAGCCCGCACTGTCAGGGGCGTTC ++ +B;CA40FF4GH>HHI!HCJGJ#:JHI7IJIFIJF##GJ!IGJJGGHG4JAGJCJJ#G#IGI?AIHCJ@AJ#JH#CBD#DD@?CD:ADFBCC?E!5C>##D +@NC_011750.1-36/2 +CGATAACGGTAACGTTGTGACCGCGCGCTTCTAATATGCCGGACATAATGGCGGTGGACTTTTTCTCGCGCCGGCAATTGAGCGCAGCGTTGATGCTGTC ++ +@=@+=CF:FHDGF#CDD#@' +@NC_011750.1-34/2 +GGCAGGGGCAGGTGGCCATCGTCCTCTCTGCCCCCGCCAACATGACCAACCACCTGGTGGCGATGATTGAAAAAACCAATAGCACCCAGGATGCATTACT ++ +@@@FADDFHHHAH92FFJ!GECAEECJG##JHDAHIJ*GJ!<*!C?DI#D=EHGJ2JJHJJGGAJ=#HBEFBIHA<#F#:<@D#!D5ECFDCCB#CD#@' +@NC_011750.1-32/2 +ACGGCGGGTGCACTTAGCAATATCGACGGTAGATTCGAGGTAAGGCCCCACTGCCAGCAGATTTTCGACCGGGTCGAGAACCGTAACGTTGTGGTAGCGC ++ +?BCF4;DDH<#3HG#HGHJ#>AGGHAE?DDII+GF?IJIG*JI#BIHICFHGIC6DHGH##DI(#>CG;7>A##C@F#(:D#EBA#I#DC8D##!#?>DC +@NC_011750.1-30/2 +TTGACCCAATATCACCGATGCGCAACGGATTTTTTGCGAACATCTGACGGGACTCGCCGCGGCCCAACCGTGATCACCGCTCGCGCAACTGCAAGAATTC ++ +B@+D1F0DAEHFGD#HA3JJI##HIFI#IGGGJH!#G#EJG#A#DBIHEFC;GEJBJGCH'J<#E;#.@D#HD>##DDD#7#@EC;,CFC?#CC##!;?5 +@NC_011750.1-28/2 +TACTCGCATTGTTGTTACCTCGTTGCCTTTGGTCGTAAAAAAAGCCCGCATTGTAAGGTGCGGGCTTTGTGCTGTGTTTCCGGTACGCTTCATCGCGCAG ++ ++CBFBDFDH#HHHEHHJJJIE#@A9!<#DDD<' +@NC_011750.1-26/2 +CACTGCCCGAACAATCAACTGCCATACAGAACATGTTCGATTTGGGCACATACCTGATCGACGAAAGCTTTCAGTTGCGCCAGCGGGAATCCCAGGTGAT ++ +BCCFFFAA#HHH+J+E#A#JJGICA#FC1#JJJIIII##IIJHJII>I#AF#IDC#FIEHIDFI;CF!DFF>DB&@+A)3DE4C;CDDA5B>D###CD#' +@NC_011750.1-24/2 +AATTACAGAGTATACAACATCCATGAAACTCATTAGCACCACCAATACCACCACCATCACCATTACCACATGTAACGGAGCGGGCTGACGCTCCCAGAAA ++ +B@@F4CFFH+B2#+?JII?JJ,?<+IJ@J#GHH#GID>H*BJ?D!F9I9DF1FICHG;JF@D8JEGHJJB#=?@D?HG##=D;ECDC,FAD8##1CD#BD +@NC_011750.1-22/2 +TCACCATTTCCACAGGTAAAGGTTCGGGCTGACGAGTACAGGAAACACAGTAAACGGCCCGCACCTGACAGTACGGGCCTTTTTTTCGACCATAAATAAC ++ +:@CAFEFB#HDAH2*;JIF#JGI#?IBIG#HIHG#B0IH:HJFG#GIJ9C2D#E##CA>' +@NC_011750.1-20/2 +CACCGTCCGCTCTGCCCCCGCCACAATCACCAACCACTTGGTGGCGATGATTGAAAAAATGATTAGCGGCCCAGATGCTTTACCCAACACAAGCGCTGCT ++ +@BCFF;FA+FHF,CEHJC+JGHD#FGIJGF1?1J9#)#D;GBHHH#DCBECGH##CDFCH>H:DD6CDD#@##BC#D#C(D' +@NC_011750.1-18/2 +GTAGATGCGAGGTAATGCCTCACTGCCAGCAGTTTTTCGACCGGATCGATAACGGTAACGTTAGGACCGCGCGCTTCTAGTTCGCTGGCCTCAATGGCGA ++ +@C+F4C!FHHHF#JCCHCJ!J0JHGC<#GIC:IE9JI:II9G9;EFG#IF#GHJB.?F:IBF###9#HBHDDBEGH:@I#J#DCH#D4D###C#9C><@D +@NC_011750.1-16/2 +ACATTTTCTCGCCACGCCAAATCAGCGCAGCGTTGTTGCAATCCGGGCTCGGCCCCAACAAACTAAGGCCATGCAGGACATGTAATATTTGGGCAACTCC ++ +CC=FFFDFHHGH2JGJ#IHIE@HJJI#IFABF;G?#?II!HBJI@BHB#<#CEG@B>C#HHC;JJD#8DBCDH#?9@CCB@>HC:E#:#@ +@NC_011750.1-14/2 +GGGCAGCGGCGAGTCCCGTCAGAAGTACAGCAAAAATATATCCAGGAGCGCTGATATTGGGTAAAGCACACTGGAAGCAAATGGGTTTTTAAAGCACCGC ++ +=C?DFF>DDHHH?JCIAIIB:D#DD#3D#:A' +@NC_011750.1-12/2 +GTTTCCTTGTTACCTTTGGTCGAAAAAAAAGCCCGCACTGTCAGGTGCGGGCCTTTTTCTGTGTTTCCTATTCGCGTCAGCTCGCACGGTGACCTGTGGT ++ +=@@#=F,!HHGHBI+J2?JIHI:#E;?CD>#DBD?5A#EBC +@NC_011750.1-6/2 +TGCCCAACCGGGATTCCCGCTGGCGCATCTGAAAACTTTCGTAGATCAGGAGGTTGCCCAAAGTAAACATCTCGTGCATGGCATAAGGCTGTTGGGGCAG ++ +@1B4FDFF=CD?2I#IJF<8##CDJ#HB#C=#>F=D#G@DHA#B#!#CCE;9#B@CC#!' +@NC_011750.1-2/2 +TTTATTGCCTTAGGTCACTAAATACTTTAACCAATACATCCATAGCGCACAGACACATAAAAATTACAGAGTACACAACATCCATGAAATGCGATAGCAC ++ +8BCDFFD)HHHH>AIIJJJJE*J#A9JH@JJ#9JDD=JIA)FA:#C==?#FCA#DD9CBCBADD?#(C###9D?BD diff -r 000000000000 -r b7b1c8bf7ae0 test-data/NC_011750.1_simulated_bracken_report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_011750.1_simulated_bracken_report.txt Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,2 @@ +name taxonomy_id taxonomy_lvl kraken_assigned_reads added_reads new_est_reads fraction_total_reads +Escherichia coli 562 S 42 1 43 1.00000 diff -r 000000000000 -r b7b1c8bf7ae0 test-data/NC_011750.1_simulated_kraken_report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_011750.1_simulated_kraken_report.txt Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,11 @@ + 4.44 2 2 U 0 unclassified + 95.56 43 0 R 1 root + 95.56 43 0 R1 131567 cellular organisms + 95.56 43 0 D 2 Bacteria + 95.56 43 0 P 1224 Proteobacteria + 95.56 43 0 C 1236 Gammaproteobacteria + 95.56 43 0 O 91347 Enterobacterales + 95.56 43 1 F 543 Enterobacteriaceae + 93.33 42 0 G 561 Escherichia + 93.33 42 0 S 562 Escherichia coli + 93.33 42 42 S1 585057 Escherichia coli IAI39 diff -r 000000000000 -r b7b1c8bf7ae0 test-data/bracken_databases.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bracken_databases.loc Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,6 @@ +# Tab separated with three columns: +# - value (Galaxy records this in the Galaxy DB) +# - name (Galaxy shows this in the UI) +# - path (folder name containing the Kraken DB) +# +test_entry "Test Database" ${__HERE__}/test_db/database100mers.kmer_distrib diff -r 000000000000 -r b7b1c8bf7ae0 test-data/reproduce_test_data.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reproduce_test_data.sh Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,29 @@ +#!/bin/bash + +# This script produces a small kraken2 database containing only a ~1kb portion each of a salmonella and ecoli genome +# It requires kraken2, art and entrez-direct (all available on bioconda) +kraken2-build --db test_db --download_taxonomy +mv test_db/taxonomy/nucl_gb.accession2taxid test_db/taxonomy/nucl_gb.accession2taxid_full +grep -e 'NC_003198.1' -e 'NC_011750.1' test_db/taxonomy/nucl_gb.accession2taxid_full > test_db/taxonomy/nucl_gb.accession2taxid +esearch -db nucleotide -query "NC_003198.1" | efetch -format fasta > NC_003198.1.fasta +esearch -db nucleotide -query "NC_011750.1" | efetch -format fasta > NC_011750.1.fasta +head -n 14 NC_003198.1.fasta > NC_003198.1_1kb.fasta +head -n 14 NC_011750.1.fasta > NC_011750.1_1kb.fasta +kraken2-build --db test_db --add-to-library NC_003198.1_1kb.fasta +kraken2-build --db test_db --add-to-library NC_011750.1_1kb.fasta +kraken2-build --db test_db --build + +# Simulate 100bp reads from ~1kb portions of genomes +art_illumina -sam -i NC_011750.1_1kb.fasta -p -m 300 -f 10 -s 10 -l 100 -o NC_011750.1_simulated_R +art_illumina -sam -i NC_003198.1_1kb.fasta -p -m 300 -f 10 -s 10 -l 100 -o NC_003198.1_simulated_R + +# Generate kraken reports +kraken2 --db test_db --report NC_011750.1_simulated_kraken_report.txt --paired NC_011750.1_simulated_R1.fastq NC_011750.1_simulated_R2.fastq +kraken2 --db test_db --report NC_003198.1_simulated_kraken_report.txt --paired NC_003198.1_simulated_R1.fastq NC_003198.1_simulated_R2.fastq + +# Build bracken kmer distribution files using default kmer-len=35 and read-len=100 +bracken-build -d test_db + +# +# est_abundance.py --kmer_distr test_db/database100mers.kmer_distrib --level S -i NC_003198.1_simulated_kraken_report.txt -o NC_003198.1_simulated_bracken_report.txt +# est_abundance.py --kmer_distr test_db/database100mers.kmer_distrib --level S -i NC_011750.1_simulated_kraken_report.txt -o NC_011750.1_simulated_bracken_report.txt diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/database.kraken --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_db/database.kraken Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,2 @@ +C NC_003198.1 220341 910 220341:169 A:67 543:23 220341:9 A:42 220341:9 543:65 220341:134 543:2 220341:356 +C NC_011750.1 585057 910 585057:11 A:41 585057:116 A:67 543:24 585057:7 A:42 585057:10 543:64 585057:134 543:2 585057:358 diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/database100mers.kmer_distrib --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_db/database100mers.kmer_distrib Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,5 @@ +mapped_taxid genome_taxids:kmers_mapped:total_genome_kmers +0 220341:2:811 585057:2:811 +543 220341:23:811 585057:24:811 +220341 220341:786:811 +585057 585057:785:811 diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/database100mers.kraken --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_db/database100mers.kraken Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,2 @@ +NC_003198.1 220341 220341 910 0:2 543:23 220341:786 +NC_011750.1 585057 585057 910 0:2 543:24 585057:785 diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/hash.k2d Binary file test-data/test_db/hash.k2d has changed diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/library/added/9C7DdW7GAD.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_db/library/added/9C7DdW7GAD.fna Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,17 @@ +>NC_003198.1 Salmonella enterica subsp. enterica serovar Typhi str. CT18, complete genome +AGAGATTACGTCTGGTTGCAAGAGATCATAACAGGGGAAATTGATTGAAAATAAATATAT +CGCCAGCAGCACATGAACAAGTTTCGGAATGTGATCAATTTAAAAATTTATTGACTTAGG +CGGGCAGATACTTTAACCAATATAGGAATACAAGACAGACAAATAAAAATGACAGAGTAC +ACAACATCCATGAACCGCATCAGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxAGGT +AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGAACAGTGCGG +GCxxxxxxxxCGACCAGAGATCACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT +ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATTCC +AGGCAAGGGCAGGTAGCGACCGTACTTTCCGCCCCCGCGAAAATTACCAACCATCTGGTG +GCGATGATTGAAAAAACTATCGGCGGCCAGGATGCTTTGCCGAATATCAGCGATGCCGAA +CGTATTTTTTCTGACCTGCTCGCAGGACTTGCCAGCGCGCAGCCGGGATTCCCGCTTGCA +CGGTTGAAAATGGTTGTCGAACAAGAATTCGCTCAGATCAAACATGTTTTGCATGGTATC +AGCCTGCTGGGTCAGTGCCCGGATAGCATCAACGCCGCGCTGATTTGCCGTGGCGAAAAA +ATGTCGATCGCGATTATGGCGGGACTCCTGGAGGCGCGTGGACATCGCGTCACGGTGATC +GATCCGGTAGAAAAACTGCTGGCGGTGGGCCATTACCTTGAATCTACCGTCGATATCGCG +GAATCGACTCGCCGTATCGCCGCCAGCCAGATCCCGGCCGATCACATGATCCTGATGGCG +GGCTTTACTG diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/library/added/9C7DdW7GAD.fna.masked diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/library/added/cWk1IBlK73.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_db/library/added/cWk1IBlK73.fna Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,17 @@ +>NC_011750.1 Escherichia coli IAI39 chromosome, complete genome +GCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTxxxxxxxGAGTGTCT +GATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGT +CACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACA +CAACATCCATGAAACGCATTAGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxAGGTA +ACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGC +xxxxxxxxCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTAC +ATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAG +GCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGC +GATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACG +TATTTTTGCCGAACTTCTGACGGGACTCGCCGCTGCCCAACCGGGATTCCCGCTGGCGCA +ACTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAG +TTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAAT +GTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACCGTTATCGA +TCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGA +GTCCACCCGCCGTATTGCGGCAAGTCGTATTCCGGCTGATCACATGGTGCTGATGGCAGG +TTTCACCGCC diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/library/added/cWk1IBlK73.fna.masked diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/library/added/prelim_map.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_db/library/added/prelim_map.txt Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,2 @@ +ACCNUM NC_011750.1 NC_011750 +ACCNUM NC_003198.1 NC_003198 diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/library/added/prelim_map_QXr8C5PiOX.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_db/library/added/prelim_map_QXr8C5PiOX.txt Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,1 @@ +ACCNUM NC_003198.1 NC_003198 diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/library/added/prelim_map_l8ftMYsZv0.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_db/library/added/prelim_map_l8ftMYsZv0.txt Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,1 @@ +ACCNUM NC_011750.1 NC_011750 diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/opts.k2d Binary file test-data/test_db/opts.k2d has changed diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/seqid2taxid.map --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_db/seqid2taxid.map Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,2 @@ +NC_003198.1 220341 +NC_011750.1 585057 diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/taxo.k2d Binary file test-data/test_db/taxo.k2d has changed diff -r 000000000000 -r b7b1c8bf7ae0 tool-data/bracken_databases.loc.sample diff -r 000000000000 -r b7b1c8bf7ae0 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,7 @@ + + + + value, name, path + +
+
diff -r 000000000000 -r b7b1c8bf7ae0 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Oct 16 16:57:55 2019 -0400 @@ -0,0 +1,8 @@ + + + + + value, name, path + +
+