Purdue University

bbmap

Link to section 'Introduction' of 'bbmap' Introduction

Bbmap is a short read aligner, as well as various other bioinformatic tools.

For more information, please check its website: https://biocontainers.pro/tools/bbmap and its home page on Sourceforge.

Link to section 'Versions' of 'bbmap' Versions

• 38.93
• 38.96

Link to section 'Commands' of 'bbmap' Commands

• addadapters.sh
• a_sample_mt.sh
• bbcountunique.sh
• bbduk.sh
• bbest.sh
• bbfakereads.sh
• bbmap.sh
• bbmapskimmer.sh
• bbmask.sh
• bbmerge-auto.sh
• bbmergegapped.sh
• bbmerge.sh
• bbnorm.sh
• bbqc.sh
• bbrealign.sh
• bbrename.sh
• bbsketch.sh
• bbsplitpairs.sh
• bbsplit.sh
• bbstats.sh
• bbversion.sh
• bbwrap.sh
• calcmem.sh
• calctruequality.sh
• callpeaks.sh
• callvariants2.sh
• callvariants.sh
• clumpify.sh
• commonkmers.sh
• comparesketch.sh
• comparevcf.sh
• consect.sh
• countbarcodes.sh
• countgc.sh
• countsharedlines.sh
• crossblock.sh
• crosscontaminate.sh
• cutprimers.sh
• decontaminate.sh
• dedupe2.sh
• dedupebymapping.sh
• dedupe.sh
• demuxbyname.sh
• diskbench.sh
• estherfilter.sh
• explodetree.sh
• filterassemblysummary.sh
• filterbarcodes.sh
• filterbycoverage.sh
• filterbyname.sh
• filterbysequence.sh
• filterbytaxa.sh
• filterbytile.sh
• filterlines.sh
• filtersam.sh
• filtersubs.sh
• filtervcf.sh
• fungalrelease.sh
• fuse.sh
• getreads.sh
• gi2ancestors.sh
• gi2taxid.sh
• gitable.sh
• grademerge.sh
• gradesam.sh
• idmatrix.sh
• idtree.sh
• invertkey.sh
• kcompress.sh
• khist.sh
• kmercountexact.sh
• kmercountmulti.sh
• kmercoverage.sh
• loadreads.sh
• loglog.sh
• makechimeras.sh
• makecontaminatedgenomes.sh
• makepolymers.sh
• mapPacBio.sh
• matrixtocolumns.sh
• mergebarcodes.sh
• mergeOTUs.sh
• mergesam.sh
• msa.sh
• mutate.sh
• muxbyname.sh
• normandcorrectwrapper.sh
• partition.sh
• phylip2fasta.sh
• pileup.sh
• plotgc.sh
• postfilter.sh
• printtime.sh
• processfrag.sh
• processspeed.sh
• randomreads.sh
• readlength.sh
• reducesilva.sh
• reformat.sh
• removebadbarcodes.sh
• removecatdogmousehuman.sh
• removehuman2.sh
• removehuman.sh
• removemicrobes.sh
• removesmartbell.sh
• renameimg.sh
• rename.sh
• repair.sh
• replaceheaders.sh
• representative.sh
• rqcfilter.sh
• samtoroc.sh
• seal.sh
• sendsketch.sh
• shred.sh
• shrinkaccession.sh
• shuffle.sh
• sketchblacklist.sh
• sketch.sh
• sortbyname.sh
• splitbytaxa.sh
• splitnextera.sh
• splitsam4way.sh
• splitsam6way.sh
• splitsam.sh
• stats.sh
• statswrapper.sh
• streamsam.sh
• summarizecrossblock.sh
• summarizemerge.sh
• summarizequast.sh
• summarizescafstats.sh
• summarizeseal.sh
• summarizesketch.sh
• synthmda.sh
• tadpipe.sh
• tadpole.sh
• tadwrapper.sh
• taxonomy.sh
• taxserver.sh
• taxsize.sh
• taxtree.sh
• testfilesystem.sh
• testformat2.sh
• testformat.sh
• tetramerfreq.sh
• textfile.sh
• translate6frames.sh
• unicode2ascii.sh
• webcheck.sh

Link to section 'Module' of 'bbmap' Module

You can load the modules by:

module load biocontainers
module load bbmap

Link to section 'Example job' of 'bbmap' Example job

To run Bbmap on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bbmap
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers bbmap

stats.sh in=SRR11234553_1.fastq > stats_out.txt
statswrapper.sh *.fastq > statswrapper_out.txt
pileup.sh in=map1.sam out=pileup_out.txt
readlength.sh in=SRR11234553_1.fastq in2=SRR11234553_2.fastq > readlength_out.txt
kmercountexact.sh in=SRR11234553_1.fastq in2=SRR11234553_2.fastq out=kmer_test.out khist=kmer.khist peaks=kmer.peak
bbmask.sh in=SRR11234553_1.fastq out=test.mark sam=map1.sam