BBTools is a suite of tools designed for the analysis of DNA and RNA sequence
data. The bundle packages version 39.19.
Usage example
The following command can be executed in the terminal to load the bundle:
The module makes the following commands available:
| addadapters.sh
addssu.sh
adjusthomopolymers.sh
alltoall.sh
analyzeaccession.sh
analyzegenes.sh
analyzesketchresults.sh
applyvariants.sh
a_sample_mt.sh
bbcms.sh
bbcountunique.sh
bbcrisprfinder.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
bbsort.sh
bbsplitpairs.sh
bbsplit.sh
bbstats.sh
bbversion.sh
bbwrap.sh
blast2sam.pl
bloomfilterparser.sh
bloomfilter.sh
bowtie2sam.pl
build_env_setup.sh
calcmem.sh
calctruequality.sh
callgenes.sh
callpeaks.sh
callvariants2.sh
callvariants.sh
cat.sh
cg2illumina.sh
checkstrand.sh
clumpify.sh
commonkmers.sh
comparegff.sh
comparelabels.sh
comparesketch.sh
comparessu.sh
comparevcf.sh
conda_build.sh
consect.sh
consensus.sh
copyfile.sh
countbarcodes2.sh
countbarcodes.sh
countduplicates.sh
countgc.sh
countsharedlines.sh
crossblock.sh
crosscontaminate.sh
cutgff.sh
cutprimers.sh
decontaminate.sh
dedupe2.sh
dedupebymapping.sh
dedupe.sh
demuxbyname.sh
demuxserver.sh
diskbench.sh
estherfilter.sh
explodetree.sh
export2sam.pl
fasta-sanitize.pl
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
findrepeats.sh
fixgaps.sh
fungalrelease.sh
fuse.sh
gbff2gff.sh
getreads.sh
gi2ancestors.sh
gi2taxid.sh
gitable.sh
gradebins.sh
grademerge.sh
gradesam.sh
icecreamfinder.sh
icecreamgrader.sh
icecreammaker.sh
idmatrix.sh
idtree.sh
interpolate_sam.pl
invertkey.sh
kapastats.sh
kcompress.sh
keepbestcopy.sh
khist.sh
kmercountexact.sh
kmercountmulti.sh
kmercoverage.sh
kmerfilterset.sh
kmerlimit2.sh
kmerlimit.sh
kmerposition.sh
kmutate.sh
lilypad.sh
loadreads.sh
loglog.sh
makechimeras.sh
makecontaminatedgenomes.sh
makepolymers.sh
makequickbinvector.sh
mapPacBio.sh
matrixtocolumns.sh
mergebarcodes.sh
mergeOTUs.sh
mergepgm.sh
mergeribo.sh
mergesam.sh
mergesketch.sh
mergesorted.sh
msa.sh
mutate.sh
muxbyname.sh
netfilter.sh
novademux.sh
novo2sam.pl
partition.sh
phylip2fasta.sh
picksubset.sh
pileup2.sh
pileup.sh
plotflowcell.sh
plotgc.sh
plothist.sh
plotreadposition.sh
polyfilter.sh
postfilter.sh
printtime.sh
processfrag.sh
processhi-c.sh
processspeed.sh
psl2sam.pl
quickbin.sh
randomgenome.sh
randomreadsmg.sh
randomreads.sh
readlength.sh
readqc.sh
reducecolumns.sh
reducesilva.sh
reformatpb.sh
reformat.sh
removebadbarcodes.sh
removecatdogmousehuman.sh
removehuman2.sh
removehuman.sh
removemicrobes.sh
removesmartbell.sh
renamebymapping.sh
renamebysketch.sh
renameimg.sh
rename.sh
repair.sh
replaceheaders.sh
representative.sh
rqcfilter2.sh
rqcfilter.sh
runhmm.sh
sam2vcf.pl
samtools.pl
samtoroc.sh
scoresequence.sh
seal.sh
sendsketch.sh
seq_cache_populate.pl
seqtovec.sh
shred.sh
shrinkaccession.sh
shuffle2.sh
shuffle.sh
sketchblacklist2.sh
sketchblacklist.sh
sketch.sh
soap2sam.pl
sortbyname.sh
splitbytaxa.sh
splitnextera.sh
splitribo.sh
splitsam4way.sh
splitsam6way.sh
splitsam.sh
stats3.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
tagandmerge.sh
taxonomy.sh
taxserver.sh
taxsize.sh
taxtree.sh
testfilesystem.sh
testformat2.sh
testformat.sh
tetramerfreq.sh
textfile.sh
tiledump.sh
train.sh
translate6frames.sh
trimcontigs.sh
unicode2ascii.sh
unzip.sh
vcf2gff.sh
webcheck.sh
wgsim_eval.pl
Xcalcmem.sh
zoom2sam.pl
|
The BBTools environment can be accessed using the bbtools_shell command.
Run pet list -t bbtools for a list of examples.
No performance notes available
Recommended resources
BBTools should be run on a system with at least 64 GB of RAM and 16 threads.
Benchmarks
No benchmarks available.
Community guides and tutorials
- No community guides available.
Official site and documentation
BBTools is licensed under the
GPLv2 license.
Primary citation
Brian Bushnell,Jonathan Rood,Esther Singer. BBMerge – Accurate paired shotgun
read merging via overlap, Published: October 26, 2017
doi
External guides and resources
- If you know of a guide/tutorial that you have found useful, please help us
share it by contacting the HPC staff at
hpc@ufs.ac.za