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
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 -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
ml biocontainers bbmap
stats.sh in=SRR11234553_1.fastq > stats_out.txt
statswrapper.sh *.fastq > statswrapper_out.txt
pileup.sh in=map1.sam out=pileup_out.txt
readlength.sh in=SRR11234553_1.fastq in2=SRR11234553_2.fastq > readlength_out.txt
kmercountexact.sh in=SRR11234553_1.fastq in2=SRR11234553_2.fastq out=kmer_test.out khist=kmer.khist peaks=kmer.peak
bbmask.sh in=SRR11234553_1.fastq out=test.mark sam=map1.sam