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/

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

39.00

BELL

39.00

GAUTSCHI

39.00

NEGISHI

39.00

SCHOLAR

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 -p wholenode        # Partition 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
module biocontainers bbtools

# Your bbtools workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers bbtools

# Your bbtools workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers bbtools

# Your bbtools workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers bbtools

# Your bbtools workflow...

#!/bin/bash
#SBATCH -A queue     # Queue 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
module biocontainers bbtools

# Your bbtools workflow...