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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

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

[…] ome (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 0.0.148) […]


Population level distribution and putative immunogenicity of cancer neoepitopes

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

[…] es 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

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

[…] has 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 each sequ […]


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

Nat Commun
PMCID: 5703905
PMID: 29180744
DOI: 10.1038/s41467-017-01992-5

[…] Illumina 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 of qual […]


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
call_split See protocol

[…] 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 pac […]


Whole Genome Sequencing Revealed Mutations in Two Independent Genes as the Underlying Cause of Retinal Degeneration in an Ashkenazi Jewish Pedigree

PMCID: 5615344
PMID: 28837078
DOI: 10.3390/genes8090210

[…] lumina,). Sequence reads were aligned using Burrows-Wheeler Aligner (BWA) [] against human genome 19 (hg19) with decoy sequences [] with the default parameters, then duplicate reads were marked using Biobambam2 []. The aligned reads were sorted by the genomic coordinate using Sambamba processor [] and stored in BAM format files. Single nucleotide polymorphism (SNPs), short insertion-deletion (INDE […]


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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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