biobambam specifications


Unique identifier OMICS_04664
Name biobambam
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
Requirements libmaus2
Maintained Yes


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



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  • person_outline German Tischler <>

biobambam article

biobambam citation

PMCID: 5224498

[…] ( and the shmirhcv318 as separate contig using the bwa-mem (v0.7.8) software (39). resulting bam files were coordinate-sorted, merged and pcr duplicates marked by biobambam (v0.0.148) software (40). the resulting bam files have an average coverage of 19.82x and 21.69x for wt and t2 31.3 cells, respectively (0x and 12.69x on the shmirhcv318 contig). […]

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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