Bbmap

Introduction

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

For more information, please check:
BioContainers: https://biocontainers.pro/tools/bbmap
Home page: https://sourceforge.net/projects/bbmap

Note

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

Versions

Cluster

Version(s)

ANVIL

38.93, 38.96

BELL

38.93, 38.96

GAUTSCHI

38.93, 38.96

NEGISHI

38.93, 38.96

SCHOLAR

38.93, 38.96

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

Module

You can load the modules by:

module load biocontainers
module load bbmap

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 bbmap 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=bbmap
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers bbmap

# Your bbmap 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=bbmap
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers bbmap

# Your bbmap 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=bbmap
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers bbmap

# Your bbmap 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=bbmap
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers bbmap

# Your bbmap workflow...

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

# Your bbmap workflow...