Bbtools

Introduction

BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.

For more information, please check:
Docker hub: https://hub.docker.com/r/staphb/bbtools
Home page: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/

Versions

  • 39.00

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

Module

You can load the modules by:

module load biocontainers
module load bbtools

Example 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