Bbmap

Introduction

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

Versions

• 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

Example job

Adjust slurm options based on job requirements (slurm cheat sheet):

#!/bin/bash
#SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
#SBATCH -N 1   # Number of nodes
#SBATCH -n 1   # Number of tasks per node
#SBATCH -c 4   # Number of CPU cores per task
#SBATCH --mem=8G       # Memory required per node
#SBATCH --job-name=bbmap       # Job name
#SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
#SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
#SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
#SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

module purge   ### Optional, but highly recommended.
module load bbmap/XXXX ### Latest version is recommended.