biobambam2

tools for early stage alignment file processing

Description

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

Upload more screenshots

Please help extend the collection of screenshots. Just make a screenshot and upload it here. You don't need to register or anything.

Hint: upload an image here from your clipboard with Ctrl-V

Homepage

Install this software package

If the package is available for the distribution you are currently using on your computer then install the software by clicking on…