@@ -342,11 +345,11 @@ **Usage** 1) Select the sequence data you wish to subtype (FASTAs or FASTQs) -2) Select subtyping scheme (e.g. *Salmonella enterica* serovar Heidelberg subtyping scheme, *Salmonella enterica* serovar Enteritidis subtyping scheme, or your own custom `biohansel` compatible subtyping scheme) +2) Select subtyping scheme (e.g. *Salmonella enterica* serovar Heidelberg, Enteritidis, Typhimurium, or Typhi subtyping scheme, or your own custom `biohansel` compatible subtyping scheme) 3) [Optional] Select your subtype metadata information table to include subtype metadata along with your subtype results 4) Click ``Execute`` -For more information, visit `the biohansel project page `_. +For more information, visit `the biohansel project page `_ or the `biohansel read the docs page `_. **Example analysis results of a single FASTA file** @@ -354,7 +357,7 @@ Contents of ``results.tab``: +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+ - | sample | scheme | scheme_version | subtype | all_subtypes | tiles_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_tiles_matching_all | n_tiles_matching_all_expected | n_tiles_matching_positive | n_tiles_matching_positive_expected | n_tiles_matching_subtype | n_tiles_matching_subtype_expected | file_path | qc_status | qc_message | + | sample | scheme | scheme_version | subtype | all_subtypes | kmers_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_kmers_matching_all | n_kmers_matching_all_expected | n_kmers_matching_positive | n_kmers_matching_positive_expected | n_kmers_matching_subtype | n_kmers_matching_subtype_expected | file_path | qc_status | qc_message | +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+ | SRR1002850_SMALL | heidelberg | 0.5.0 | 2.2.2.2.1.4 | 2; 2.2; 2.2.2; 2.2.2.2; 2.2.2.2.1; 2.2.2.2.1.4 | 2154958-2.2.2.2.1.4; 1037658-2.2.2.2.1.4; 3785187-2.2.2.2.1.4 | True | | 202 | 202 | 17 | 17 | 3 | 3 | SRR1002850_SMALL.fasta | PASS | | +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+ @@ -363,7 +366,7 @@ Contents of ``match_results.tab``: +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+ - | tilename | seq | is_revcomp | contig_id | match_index | refposition | subtype | is_pos_tile | sample | file_path | scheme | scheme_version | qc_status | qc_message | + | kmername | seq | is_revcomp | contig_id | match_index | refposition | subtype | is_pos_kmer | sample | file_path | scheme | scheme_version | qc_status | qc_message | +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+ | 2154958-2.2.2.2.1.4 | GGCGCGCCACGGTTACTCCCCGGTGGTCAGCCG | True | NODE_1_length_726282_cov_40.4705_ID_1 | 13732 | 2154958 | 2.2.2.2.1.4 | True | SRR1002850_SMALL | SRR1002850_SMALL.fasta | heidelberg | 0.5.0 | PASS | | +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+ @@ -380,7 +383,7 @@ Contents of ``results.tab``: +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+ - | sample | scheme | scheme_version | subtype | all_subtypes | tiles_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_tiles_matching_all | n_tiles_matching_all_expected | n_tiles_matching_positive | n_tiles_matching_positive_expected | n_tiles_matching_subtype | n_tiles_matching_subtype_expected | file_path | avg_tile_coverage | qc_status | qc_message | + | sample | scheme | scheme_version | subtype | all_subtypes | kmers_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_kmers_matching_all | n_kmers_matching_all_expected | n_kmers_matching_positive | n_kmers_matching_positive_expected | n_kmers_matching_subtype | n_kmers_matching_subtype_expected | file_path | avg_kmer_coverage | qc_status | qc_message | +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+ | SRR5646583_SMALL | heidelberg | 0.5.0 | 2.2.1.1.1.1 | 2; 2.2; 2.2.1; 2.2.1.1; 2.2.1.1.1; 2.2.1.1.1.1 | 1983064-2.2.1.1.1.1; 4211912-2.2.1.1.1.1 | True | | 202 | 202 | 20 | 20 | 2 | 2 | ['SRR5646583_SMALL_1.fastq', 'SRR5646583_SMALL_2.fastq'] | 42.631 | PASS | | +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+ @@ -388,7 +391,7 @@ Contents of ``match_results.tab``: +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+ - | tilename | seq | freq | refposition | subtype | is_pos_tile | is_kmer_freq_okay | sample | scheme | scheme_version | qc_status | qc_message | + | kmername | seq | freq | refposition | subtype | is_pos_kmer | is_kmer_freq_okay | sample | scheme | scheme_version | qc_status | qc_message | +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+ | negative4642573-1.2 | TACCAGGAAGTGCTGGAAGAGTTTAACGAACAT | 62 | 4642573 | 1.2 | False | True | SRR5646583_SMALL | heidelberg | 0.5.0 | PASS | | +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+ @@ -424,8 +427,8 @@ @ARTICLE{a1, title = {A robust genotyping scheme for Salmonella enterica serovar Heidelberg clones circulating in North America}, - author = {Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Marisa Rankin, Matthew Gopez, Chad R. Laing, Philip Mabon, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Joanne MacKinnon, Roger Johnson, John H.E. Nash}, - url = {https://github.com/phac-nml/bio_hansel} + author = {Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Marisa Rankin, Matthew Gopez, Chad R. Laing, Philip Mabon, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, David Son, Darian Hole, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Joanne MacKinnon, Roger Johnson, John H.E. Nash}, + url = {https://github.com/phac-nml/biohansel} } } diff -r 3360158bb0c5 -r 4fa9d5e748d4 test-data/SRR1002850_SMALL.fasta-match_results.tab --- a/test-data/SRR1002850_SMALL.fasta-match_results.tab Mon May 13 09:42:08 2019 -0400 +++ b/test-data/SRR1002850_SMALL.fasta-match_results.tab Tue May 21 15:05:40 2019 -0400 @@ -1,4 +1,4 @@ -tilename seq is_revcomp contig_id match_index refposition subtype is_pos_tile sample file_path scheme scheme_version qc_status qc_message +kmername seq is_revcomp contig_id match_index refposition subtype is_pos_kmer sample file_path scheme scheme_version qc_status qc_message 2154958-2.2.2.2.1.4 GGCGCGCCACGGTTACTCCCCGGTGGTCAGCCG True NODE_1_length_726282_cov_40.4705_ID_1 13732 2154958 2.2.2.2.1.4 True SRR1002850_SMALL SRR1002850_SMALL.fasta heidelberg 0.5.0 PASS negative2131791-2.2.3.1.3 GCTGGGCGAAATGATGCAGTTCACCACTTGCTC True NODE_1_length_726282_cov_40.4705_ID_1 36900 2131791 2.2.3.1.3 False SRR1002850_SMALL SRR1002850_SMALL.fasta heidelberg 0.5.0 PASS 2069216-2.2.2 ATACTTAGGCTGTCAGTAACCCGTGAGGTAGTG True NODE_1_length_726282_cov_40.4705_ID_1 99475 2069216 2.2.2 True SRR1002850_SMALL SRR1002850_SMALL.fasta heidelberg 0.5.0 PASS diff -r 3360158bb0c5 -r 4fa9d5e748d4 test-data/SRR1002850_SMALL.fasta-results.tab --- a/test-data/SRR1002850_SMALL.fasta-results.tab Mon May 13 09:42:08 2019 -0400 +++ b/test-data/SRR1002850_SMALL.fasta-results.tab Tue May 21 15:05:40 2019 -0400 @@ -1,2 +1,2 @@ -sample scheme scheme_version subtype all_subtypes tiles_matching_subtype are_subtypes_consistent inconsistent_subtypes n_tiles_matching_all n_tiles_matching_all_expected n_tiles_matching_positive n_tiles_matching_positive_expected n_tiles_matching_subtype n_tiles_matching_subtype_expected file_path qc_status qc_message +sample scheme scheme_version subtype all_subtypes kmers_matching_subtype are_subtypes_consistent inconsistent_subtypes n_kmers_matching_all n_kmers_matching_all_expected n_kmers_matching_positive n_kmers_matching_positive_expected n_kmers_matching_subtype n_kmers_matching_subtype_expected file_path qc_status qc_message SRR1002850_SMALL heidelberg 0.5.0 2.2.2.2.1.4 2; 2.2; 2.2.2; 2.2.2.2; 2.2.2.2.1; 2.2.2.2.1.4 2154958-2.2.2.2.1.4; 1037658-2.2.2.2.1.4; 3785187-2.2.2.2.1.4 True 202 202 17 17 3 3 SRR1002850_SMALL.fasta PASS diff -r 3360158bb0c5 -r 4fa9d5e748d4 test-data/SRR5646583_SMALL-match_results.tab --- a/test-data/SRR5646583_SMALL-match_results.tab Mon May 13 09:42:08 2019 -0400 +++ b/test-data/SRR5646583_SMALL-match_results.tab Tue May 21 15:05:40 2019 -0400 @@ -1,4 +1,4 @@ -tilename seq freq refposition subtype is_pos_tile is_kmer_freq_okay sample scheme scheme_version qc_status qc_message +kmername seq freq refposition subtype is_pos_kmer is_kmer_freq_okay sample scheme scheme_version qc_status qc_message negative4642573-1.2 TACCAGGAAGTGCTGGAAGAGTTTAACGAACAT 62 4642573 1.2 False True SRR5646583_SMALL heidelberg 0.5.0 PASS 21097-2.2.1.1.1 GCAAATCGCGCCAGTCAAGTCCTCTTTTACCGT 42 21097 2.2.1.1.1 True True SRR5646583_SMALL heidelberg 0.5.0 PASS negative3647258-2.2.2.2.2.1 TACGGGTAACTGTTATCGGTAACATTGTCCAAC 64 3647258 2.2.2.2.2.1 False True SRR5646583_SMALL heidelberg 0.5.0 PASS diff -r 3360158bb0c5 -r 4fa9d5e748d4 test-data/SRR5646583_SMALL-results.tab --- a/test-data/SRR5646583_SMALL-results.tab Mon May 13 09:42:08 2019 -0400 +++ b/test-data/SRR5646583_SMALL-results.tab Tue May 21 15:05:40 2019 -0400 @@ -1,2 +1,2 @@ -sample scheme scheme_version subtype all_subtypes tiles_matching_subtype are_subtypes_consistent inconsistent_subtypes n_tiles_matching_all n_tiles_matching_all_expected n_tiles_matching_positive n_tiles_matching_positive_expected n_tiles_matching_subtype n_tiles_matching_subtype_expected file_path avg_tile_coverage qc_status qc_message +sample scheme scheme_version subtype all_subtypes kmers_matching_subtype are_subtypes_consistent inconsistent_subtypes n_kmers_matching_all n_kmers_matching_all_expected n_kmers_matching_positive n_kmers_matching_positive_expected n_kmers_matching_subtype n_kmers_matching_subtype_expected file_path avg_kmer_coverage qc_status qc_message SRR5646583_SMALL heidelberg 0.5.0 2.2.1.1.1.1 2; 2.2; 2.2.1; 2.2.1.1; 2.2.1.1.1; 2.2.1.1.1.1 1983064-2.2.1.1.1.1; 4211912-2.2.1.1.1.1 True 202 202 20 20 2 2 ['SRR5646583_SMALL_1.fastq', 'SRR5646583_SMALL_2.fastq'] 42.631 PASS diff -r 3360158bb0c5 -r 4fa9d5e748d4 test-data/SRR5646583_SMALL-tech_results.tab --- a/test-data/SRR5646583_SMALL-tech_results.tab Mon May 13 09:42:08 2019 -0400 +++ b/test-data/SRR5646583_SMALL-tech_results.tab Tue May 21 15:05:40 2019 -0400 @@ -1,2 +1,2 @@ -sample subtype avg_tile_coverage qc_status qc_message +sample subtype avg_kmer_coverage qc_status qc_message SRR5646583_SMALL 2.2.1.1.1.1 42.631 PASS