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1 DATA
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2 #Illumina paired end reads supplied as <two-character prefix> <fragment mean> <fragment stdev> <forward_reads> <reverse_reads>
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3 #if single-end, do not specify <reverse_reads>
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4 #MUST HAVE Illumina paired end reads to use MaSuRCA
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5 #PE= pe 500 50 /FULL_PATH/frag_1.fastq /FULL_PATH/frag_2.fastq
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6 PE= pe MEAN STDDEV INPUTREAD1 INPUTREAD2
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7 #Illumina mate pair reads supplied as <two-character prefix> <fragment mean> <fragment stdev> <forward_reads> <reverse_reads>
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8 #JUMP= sh 3600 200 /FULL_PATH/short_1.fastq /FULL_PATH/short_2.fastq
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9 #pacbio OR nanopore reads must be in a single fasta or fastq file with absolute path, can be gzipped
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10 #if you have both types of reads supply them both as NANOPORE type
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11 #PACBIO=/FULL_PATH/pacbio.fa
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12 #PACBIO=INPUTREADLONG
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13 #NANOPORE=/FULL_PATH/nanopore.fa
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14 #NANOPORE=INPUTREADLONG
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15 #Other reads (Sanger, 454, etc) one frg file, concatenate your frg files into one if you have many
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16 #OTHER=/FULL_PATH/file.frg
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17 #synteny-assisted assembly, concatenate all reference genomes into one reference.fa; works for Illumina-only data
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18 #REFERENCE=REF
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19 END
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20
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21 PARAMETERS
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22 #PLEASE READ all comments to essential parameters below, and set the parameters according to your project
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23 #set this to 1 if your Illumina jumping library reads are shorter than 100bp
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24 EXTEND_JUMP_READS=0
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25 #this is k-mer size for deBruijn graph values between 25 and 127 are supported, auto will compute the optimal size based on the read data and GC content
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26 GRAPH_KMER_SIZE = auto
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27 #set this to 1 for all Illumina-only assemblies
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28 #set this to 0 if you have more than 15x coverage by long reads (Pacbio or Nanopore) or any other long reads/mate pairs (Illumina MP, Sanger, 454, etc)
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29 USE_LINKING_MATES = 0
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30 #specifies whether to run the assembly on the grid
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31 USE_GRID=0
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32 #specifies grid engine to use SGE or SLURM
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33 GRID_ENGINE=SLURM
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34 #specifies queue (for SGE) or partition (for SLURM) to use when running on the grid MANDATORY
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35 GRID_QUEUE=defq
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36 #batch size in the amount of long read sequence for each batch on the grid
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37 GRID_BATCH_SIZE=500000000
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38 #use at most this much coverage by the longest Pacbio or Nanopore reads, discard the rest of the reads
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39 #can increase this to 30 or 35 if your reads are short (N50<7000bp)
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40 LHE_COVERAGE=25
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41 #set to 0 (default) to do two passes of mega-reads for slower, but higher quality assembly, otherwise set to 1
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42 MEGA_READS_ONE_PASS=0
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43 #this parameter is useful if you have too many Illumina jumping library mates. Typically set it to 60 for bacteria and 300 for the other organisms
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44 LIMIT_JUMP_COVERAGE = 300
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45 #these are the additional parameters to Celera Assembler. do not worry about performance, number or processors or batch sizes -- these are computed automatically.
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46 #CABOG ASSEMBLY ONLY: set cgwErrorRate=0.25 for bacteria and 0.1<=cgwErrorRate<=0.15 for other organisms.
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47 CA_PARAMETERS = cgwErrorRate=0.15
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48 #CABOG ASSEMBLY ONLY: whether to attempt to close gaps in scaffolds with Illumina or long read data
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49 CLOSE_GAPS=1
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50 #number of cpus to use, set this to the number of CPUs/threads per node you will be using
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51 NUM_THREADS = GALAXY_SLOTS
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52 #this is mandatory jellyfish hash size -- a safe value is estimated_genome_size*20
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53 JF_SIZE = JELLYFISHSIZE
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54 #ILLUMINA ONLY. Set this to 1 to use SOAPdenovo contigging/scaffolding module.
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55 #Assembly will be worse but will run faster. Useful for very large (>=8Gbp) genomes from Illumina-only data
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56 SOAP_ASSEMBLY=0
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57 #If you are doing Hybrid Illumina paired end + Nanopore/PacBio assembly ONLY (no Illumina mate pairs or OTHER frg files).
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58 #Set this to 1 to use Flye assembler for final assembly of corrected mega-reads.
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59 #A lot faster than CABOG, AND QUALITY IS THE SAME OR BETTER.
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60 #Works well even when MEGA_READS_ONE_PASS is set to 1.
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61 #DO NOT use if you have less than 15x coverage by long reads.
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62 FLYE_ASSEMBLY=0
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63 END
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