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biobambam specifications


Unique identifier OMICS_04664
Name biobambam
Alternative name biobambam2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM
Operating system Unix/Linux, Mac OS
Programming languages C++, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0.87
Stability Stable
Maintained Yes


  • bamcollate2
  • bammarkduplicates
  • bammaskflags
  • bamrecompress
  • bamsormadup
  • bamsort
  • bamtofastq




No version available



  • person_outline German Tischler <>

Publication for biobambam

biobambam citations


Genomic features of renal cell carcinoma with venous tumor thrombus

PMCID: 5945671
PMID: 29748622
DOI: 10.1038/s41598-018-25544-z

[…] (build 37, version hs37d5), using bwa mem (version 0.7.8 with minimum base quality threshold set to zero [−t 0] and remaining settings left at default values), followed by coordinate-sorting with bamsort (with compression option set to fast (1)) and marking duplicate read pairs with bammarkduplicates (with compression option set to best (9)) (both part of the biobambam package version […]


Population level distribution and putative immunogenicity of cancer neoepitopes

PMCID: 5899330
PMID: 29653567
DOI: 10.1186/s12885-018-4325-6

[…] of response to immunotherapy in melanoma patients []. reads were aligned against the grch37d5 reference genome using the sanger cgpmap workflow []. this workflow uses bwa-mem (v0.7.15–1140) [] and biobambam2 (v2.0.69) [] to generate genome coordinate-sorted alignments with duplicates marked. realignment around indels and base recalibration were performed using genome analysis toolkit (v3.6) […]


Analyzing Immunoglobulin Repertoires

PMCID: 5861150
PMID: 29593723
DOI: 10.3389/fimmu.2018.00462

[…] to be converted to fasta or fastq format either by running scripts that are part of the software platform (sffinfo-roche; bcl2fastq-illumina) or by using one of the many freely available scripts (bamtofastq, sff_extract). fasta and fastq are the two common input formats for most analysis programs. fasta format consists of a list of sequences with a unique identification tag preceding […]


Variant ribosomal RNA alleles are conserved and exhibit tissue specific expression

PMCID: 5829973
PMID: 29503865
DOI: 10.1126/sciadv.aao0665

[…] (gatk) best practices pipeline for variant discovery. namely, the bam file was further prepared with the tools cleansam and addorreplacereadgroups in picard, and read duplicates were marked with biobambam. reads were realigned using the tool realignertargetcreator from gatk, where both the dbsnp variant database and the individual-/strain-specific variant sites were used for the “-known” […]


Stem cell senescence drives age attenuated induction of pituitary tumours in mouse models of paediatric craniopharyngioma

PMCID: 5703905
PMID: 29180744
DOI: 10.1038/s41467-017-01992-5
call_split See protocol

[…] platform at the wellcome trust sanger institute at 30× depth. raw pair end sequencing reads were aligned with bwa-mem to the grcm38 mouse reference genome. duplicated reads were marked using biobambam. somatic variants were detected using caveman, an expectation maximisation-based somatic substitution-detection algorithm. detected somatic variants were then filtered using an array […]


Complete genome sequence of native Bacillus cereus strains isolated from intestinal tract of the crab Ucides sp.

PMCID: 5723261
PMID: 29234696
DOI: 10.1016/j.dib.2017.11.049

[…] technologies). the isps were loaded and sequenced on a 318 chip (life technologies)., raw sequence reads were obtained from the ion torrent server in bam format and converted to fastq using the bamtofastq program from the bedtools package . reads with more than 20% of the bases with phred score (q) smaller than 20 where removed using the fastq_quality_filter script from the fastx-toolkit […]

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biobambam institution(s)
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
biobambam funding source(s)
Supported by the Wellcome Trust.

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