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Please note that development on biobambam has stopped on this repository. Please see biobambam2 at for recent developments.

This package contains some tools for processing BAM files including

  • bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name
  • bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field
  • bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column
  • bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading.
  • bamsort: reads BAM and writes BAM resorted by coordinates or query name
  • bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name

A short list of options is available for each program by calling it with the -h parameter, e.g.

bamsort -h


The biobambam source code is hosted on github:

Compilation of biobambam

biobambam needs libmaus [] . When libmaus is installed in ${LIBMAUSPREFIX} then biobambam can be compiled and installed in ${HOME}/biobambam using

- autoreconf -i -f
- ./configure --with-libmaus=${LIBMAUSPREFIX} \
- make install