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Package: biobambam2 (2.0.183+ds-1)

tools for early stage alignment file processing

This package contains some tools for processing BAM files, including 

  bamsormadup:  parallel sorting and duplicate marking
  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

Other Packages Related to biobambam2

  • depends
  • recommends
  • suggests
  • dep: libc6 (>= 2.34)
    GNU C Library: Shared libraries
    also a virtual package provided by libc6-udeb
  • dep: libgcc-s1 (>= 3.3.1) [not amd64]
    GCC support library
    dep: libgcc-s1 (>= 3.4) [amd64]
  • dep: libgomp1 (>= 6)
    GCC OpenMP (GOMP) support library
  • dep: libmaus2-2 (>= 2.0.806+ds)
    collection of data structures and algorithms for biobambam
  • dep: libstdc++6 (>= 11)
    GNU Standard C++ Library v3
  • dep: zlib1g (>= 1:1.1.4)
    compression library - runtime

Download biobambam2

Download for all available architectures
Architecture Package Size Installed Size Files
amd64 9,479.0 kB55146 kB [list of files]
arm64 8,585.2 kB48926 kB [list of files]
ppc64el 9,053.3 kB64666 kB [list of files]