0.36 Burrows-Wheeler Alignment Tool. (Make sure no white space exists in any of the alphabet input fields on this page. This does not apply to 'Enter your data below' field.) 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_comet 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_comet 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" . "nodes=1\\n" 0 inputs Input Files 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" queryin Query File 1 query1.fq.gz queryinpair Query File 2 (paired reads) query2.fq.gz SAM_NAME Output File Name aln.sam index BWA indexing settings buildindex perl "bwa_comet" 10 Pvalue Submitting a single interleaved fastq? perl !defined $queryinpair perl ($value) ? "-p":"" 0 11 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 memopts BWA mem options Pvalue2 Submitting a single interleaved fastq? perl !defined $queryinpair perl ($value) ? "-p":"" 0 51 stdoutfile std.out all_results *