Introduction ~~~~~~~~ BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.
Docker hub: https://hub.docker.com/r/staphb/bbtools
Home page: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/
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Commands ~~~~~~~ - Xcalcmem.sh - a_sample_mt.sh - addadapters.sh - addssu.sh - adjusthomopolymers.sh - alltoall.sh - analyzeaccession.sh - analyzegenes.sh - analyzesketchresults.sh - applyvariants.sh - bbcms.sh - bbcountunique.sh - bbduk.sh - bbest.sh - bbfakereads.sh - bbmap.sh - bbmapskimmer.sh - bbmask.sh - bbmerge-auto.sh - bbmerge.sh - bbnorm.sh - bbrealign.sh - bbrename.sh - bbsketch.sh - bbsplit.sh - bbsplitpairs.sh - bbstats.sh - bbversion.sh - bbwrap.sh - bloomfilter.sh - calcmem.sh - calctruequality.sh - callgenes.sh - callpeaks.sh - callvariants.sh - callvariants2.sh - clumpify.sh - commonkmers.sh - comparegff.sh - comparesketch.sh - comparessu.sh - comparevcf.sh - consect.sh - consensus.sh - countbarcodes.sh - countgc.sh - countsharedlines.sh - crossblock.sh - crosscontaminate.sh - cutgff.sh - cutprimers.sh - decontaminate.sh - dedupe.sh - dedupe2.sh - dedupebymapping.sh - demuxbyname.sh - diskbench.sh - estherfilter.sh - explodetree.sh - fetchproks.sh - filterassemblysummary.sh - filterbarcodes.sh - filterbycoverage.sh - filterbyname.sh - filterbysequence.sh - filterbytaxa.sh - filterbytile.sh - filterlines.sh - filterqc.sh - filtersam.sh - filtersilva.sh - filtersubs.sh - filtervcf.sh - fixgaps.sh - fungalrelease.sh - fuse.sh - gbff2gff.sh - getreads.sh - gi2ancestors.sh - gi2taxid.sh - gitable.sh - grademerge.sh - gradesam.sh - icecreamfinder.sh - icecreamgrader.sh - icecreammaker.sh - idmatrix.sh - idtree.sh - invertkey.sh - kapastats.sh - kcompress.sh - keepbestcopy.sh - khist.sh - kmercountexact.sh - kmercountmulti.sh - kmercoverage.sh - kmerfilterset.sh - kmerlimit.sh - kmerlimit2.sh - kmerposition.sh - kmutate.sh - lilypad.sh - loadreads.sh - loglog.sh - makechimeras.sh - makecontaminatedgenomes.sh - makepolymers.sh - mapPacBio.sh - matrixtocolumns.sh - mergeOTUs.sh - mergebarcodes.sh - mergepgm.sh - mergeribo.sh - mergesam.sh - mergesketch.sh - mergesorted.sh - msa.sh - mutate.sh - muxbyname.sh - partition.sh - phylip2fasta.sh - pileup.sh - plotflowcell.sh - plotgc.sh - postfilter.sh - printtime.sh - processfrag.sh - processhi-c.sh - processspeed.sh - randomgenome.sh - randomreads.sh - readlength.sh - readqc.sh - reducesilva.sh - reformat.sh - reformatpb.sh - removebadbarcodes.sh - removecatdogmousehuman.sh - removehuman.sh - removehuman2.sh - removemicrobes.sh - removesmartbell.sh - rename.sh - renameimg.sh - repair.sh - replaceheaders.sh - representative.sh - rqcfilter.sh - rqcfilter2.sh - runhmm.sh - samtoroc.sh - seal.sh - sendsketch.sh - shred.sh - shrinkaccession.sh - shuffle.sh - shuffle2.sh - sketch.sh - sketchblacklist.sh - sketchblacklist2.sh - sortbyname.sh - splitbytaxa.sh - splitnextera.sh - splitribo.sh - splitsam.sh - splitsam4way.sh - splitsam6way.sh - stats.sh - statswrapper.sh - streamsam.sh - subsketch.sh - summarizecontam.sh - summarizecoverage.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 - testformat.sh - testformat2.sh - tetramerfreq.sh - textfile.sh - translate6frames.sh - unicode2ascii.sh - unzip.sh - vcf2gff.sh - webcheck.sh
You can load the modules by:
module load biocontainers
module load bbtoolsExample job ~~~~~ .. warning:: Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run bbtools on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bbtools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers bbtools