0.36 Burrows-Wheeler Alignment Tool. Assembly:Assemble_reads http://bio-bwa.sourceforge.net/ bwa_xsede dbin Database sequences (FASTA format) ref_genome.fasta command_line_single perl !defined $queryinpair perl "&& bwa_expanse mem -M -t 16" 50 command_line_single2 perl !defined $queryinpair perl "ref_genome.fasta query1.fq.gz > $SAM_NAME" 70 command_line_paired perl defined $queryinpair perl "&& bwa_expanse mem -M -t 16 " 50 command_line_paired2 perl defined $queryinpair perl " ref_genome.fasta query1.fq.gz query2.fq.gz > $SAM_NAME" 70 bwa_scheduler scheduler.conf perl "threads_per_process=12\\n" . "node_exclusive=0\\n" . "mem=23G\\n" . "nodes=1\\n" 0 runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) 0.25 Estimate the maximum time your job will need to run. We recommend testimg initially with a < 0.5hr test run because Jobs set for 0.5 h or less depedendably run immediately in the "debug" queue. Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may run sooner than jobs configured for the full 168 hours. Maximum Hours to Run must be less than 168 perl $runtime > 168.0 Maximum Hours to Run must be greater than 0.1 perl $runtime < 0.1 The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x $runtime cpu hours perl $runtime ne 0 perl "runhours=$value\\n" specify_pairedendreads Input is paired end reads (uncheck for single reads) 1 specify_interleaved Input is one interleaved, paired end file (-p) perl ($value) ? "-p":"" 0 51 Assume the first input query file is interleaved paired-end FASTA/Q. See the command description for details. queryin Query File 1(forward reads or interleaved reads) query1.fq.gz Please select a read file perl !defined $queryin queryinpair perl $specify_interleaved || $specify_pairedendreads Query File 2 (reverse reads) query2.fq.gz Please select a reverse reads file perl !defined $queryinpair && !$specify_interleaved SAM_NAME Output File Name aln.sam index BWA indexing settings buildindex perl "bwa_expanse" 10 specify_indexalg Indexing algorithm is is bwtsw bwtsw is perl "index -a $value" is - linear-time algorithm for constructing suffix array. It requires 5.37N memory where N is the size of the database. IS is moderately fast, but does not work with database larger than 2GB. bwtsw - Algorithm implemented in BWT-SW. This method works with the whole human genome, but it does not work with database smaller than 10MB and it is usually slower than IS. 12 colorspace Build color-space index? perl ($value ? "-c":"") 0 13 buildindex2 perl "ref_genome.fasta" 14 inoutopts Input/Output options specify_headerline Read group header line (-R) perl (defined $value) ? "-R $value":"" Complete read group header line. ’\t’ can be used in STR and will be converted to a TAB in the output SAM. The read group ID will be attached to every read in the output. An example is @RG\tID:foo\tSM:bar . [null] 51 insert_headerstring Insert String to header (-H) perl ($value) ? "-H $value":"" 51 specify_verbosity Verbosity level: (-v) 1 1 2 2 3 3 4 4 perl ($value) ? "-v $value":"" 1 52 1=error, 2=warning, 3=message, 4+=debugging [3] specify_minscore Minimum score to output (-T) perl ($value ne $vdef) ? "-T $value":"" 30 52 specify_minscoremin If there are less than this number of hits with score >80% (-h INT) 5 53 You can set a value using such that if there are -h hits with score >80% of the max score (200 by default), output will all be in XA. The box below this one allows you to set the maximum score for -h specify_maxscore Of this max score, output all in XA (-h INT,INT) 200 53 You can also set the maximum score for -h using this space. specify_minscoreonly perl defined $specify_minscoremin && !defined $specify_maxscore perl "-h $specify_minscoremin" 54 specify_maxminscore perl defined $specify_minscoremin && defined $specify_maxscore perl "-h $specify_minscoremin,$specify_maxscore" 54 output_all Output all alignments for SE or unpaired PE perl $value ? "-a":"" 55 Output all found alignments for single-end or unpaired paired-end reads. These alignments will be flagged as secondary alignments append_comment Append FASTA/FASTQ comment to SAM output (-C) perl $value ? "-C":"" 56 Append FASTA/Q comment to SAM output. This option can be used to transfer read meta information (e.g. barcode) to the SAM output. Note that the FASTA/Q comment (the string after a space in the header line) must conform the SAM spec (e.g. BC:Z:CGTAC). Malformed comments lead to incorrect SAM output. output_refheader Output the reference FASTA header in the XR tag (-V) perl $value ? "-V":"" 56 use_softclipping Use soft clipping for supplementary alignments (-Y) perl $value ? "-Y":"" 57 mark_shorthits Mark shorter split hits as secondary (-M) perl $value ? "-M":"" 58 For Picard compatibility specify_mean Specify the mean of insert size distribution (-I) For Picard compatibility specify_sd Specify the standard deviation of insert size distribution (-I) perl defined $specify_mean specify_max Specify the max of insert size distribution (-I) perl defined $specify_sd specify_min Specify the min of insert size distribution (-I) perl defined $specify_max specify_meansdetc1 58 perl defined $specify_mean && !defined $specify_sd perl "-I $specify_mean" specify_meansdetc2 58 perl defined $specify_sd && !defined $specify_max perl "-I $specify_mean,$specify_sd" specify_meansdetc3 58 perl defined $specify_max && !defined $specify_min perl "-I $specify_mean,$specify_sd,$specify_max" specify_meansdetc4 58 perl defined $specify_min perl "-I $specify_mean,$specify_sd,$specify_max,$specify_min" scoreopts Scoring options specify_matchscore Score for a sequence match (-A) perl ($specify_matchscore ne $vdef) ? "-A $specify_matchscore":"" 1 65 specify_mispenalty Score for a sequence match (-B) perl ($specify_mispenalty ne $vdef) ? "-B $specify_mispenalty":"" 4 65 specify_gapdpenalty Gap open penalties for deletions -O) 6 specify_gapipenalty Gap open penalties for insertions (-O) 6 specify_gappenaltystring perl $specify_gapdpenalty ne 6 || $specify_gapipenalty ne 6 perl "-O $specify_gapdpenalty,$specify_gapipenalty" 65 specify_gapextpenalty Gap extension penalty for deletion (-E) 1 specify_gapextpenalty2 Gap extension penalty for insertion (-E) 1 specify_gappenaltystring perl $specify_gapextpenalty ne 1 || $specify_gapextpenalty2 ne 1 perl "-E $specify_gapextpenalty,$specify_gapextpenalty2" 65 specify_endclippenalty Penalty for 5 prime- end clipping (-L) 5 specify_endclippenalty2 Penalty for 3 prime- end clipping (-L) 5 specify_endclippenaltyhidden perl $specify_endclippenalty ne 5 || $specify_endclippenalty2 ne 5 perl "-L $specify_endclippenalty,$specify_endclippenalty2" 65 specify_unpairedpenalty Penalty for an unpaired read pair (-U) perl ($value ne $vdef) ? "-U $value":"" 17 65 specify_readtype Read type (-x) pacbio PacBio reads to ref ont2d Oxford Nanopore 2D-reads to ref intractg Intra-species contigs to ref perl (defined $value) ? "-x $value":"" Setting -x changes multiple parameters unless overriden [null]. pacbio: -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0 (PacBio reads to ref) ont2d: -k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0 (Oxford Nanopore 2D-reads to ref) intractg: -B9 -O16 -L5 (intra-species contigs to ref) 65 algopts Algorithmic options specify_minseedlength Minimum seed length (-k) perl ($value ne $vdef) ? "-k $value":"" 19 65 specify_babandwidth Band width for banded alignment (-w) perl ($value ne $vdef) ? "-w $value":"" 100 66 specify_oddropoff Off-diagonal X-dropoff (-d) perl ($value ne $vdef) ? "-d $value":"" 100 68 specify_internalseeds Look for internal seeds inside a seed longer than {-k} (-d) perl ($value ne $vdef) ? "-d $value":"" 1.5 69 specify_seedoccurrence Seed occurrence for the 3rd round seeding (-y) perl ($value ne $vdef) ? "-y $value":"" 20 70 specify_skipseeds Skip seeds with more than INT occurrence (-c) perl ($value ne $vdef) ? "-c $value":"" 500 71 specify_dropchains Drop chains shorter than this fraction of the longest overlapping chain (-D) perl ($value ne $vdef) ? "-D $value":"" 0.5 72 specify_discardchains Discard a chain if seeded bases shorter than this (-W) perl ($value ne $vdef) ? "-D $value":"" 0 72 specify_mostrounds Perform at most this many rounds of mate r-kes for each read (-m) perl ($value ne $vdef) ? "-m $value":"" 50 73 stdoutfile std.out all_results *