mosaik samtools MosaikAligner | sed -e 's/\x1b\[[[:digit:]]\{1,2\}\(;[[:digit:]]\{1,2\}\)\{0,1\}m//g' | grep -o 'MosaikAligner [[:digit:].]\{1,\}' #set $processors = '-p ${GALAXY_SLOTS:-4}' MosaikBuild -fr #if $genomeSource.refGenomeSource == 'indexed': ${genomeSource.indexReference.fields.path} #else: ${genomeSource.historyReference} #end if -oa mosaik_ref_file; MosaikBuild -q $reads #if $paired.kind == 'single' #set $ls_string = '' #else -q2 ${paired.reads2} -mfl ${paired.mfl} #set $ls_string = '-ls %s' % $paired.ls #end if -st $st -out mosaik_reads_file; MosaikAligner -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file $ls_string -mm $mm -mhp $mhp -act $act -bw $bw $processors -hs 15; MosaikText -in mosaik_aligned_file -$outFormat sam_bam_file; #if str($outFormat) == 'bam': samtools sort sam_bam_file sorted_bam; mv sorted_bam.bam $output #else: gunzip sam_bam_file.gz; mv sam_bam_file $output #end if Use a built-in index Use one from the history SAM BAM 454 Illumina Solid Sanger Helicos Single-end Paired-end

This tool uses Mosaik to align reads to a reference sequence. 10.1371/journal.pone.0090581