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Repository seq_filter_by_mapping

Name: seq_filter_by_mapping

Owner: peterjc

Synopsis: Filter sequencing reads using SAM/BAM mapping files

Detailed description:

This tool is a short Python script (using Biopython library functions) which divides
a FASTA, FASTQ, or SFF file in two, those sequences which do or do not map according
to given SAM/BAM file(s).

Example uses include mapping of FASTQ reads against a known contaminant in order
to remove reads prior to a de novo assembly.

See https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping

Content homepage: https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping

Development repository: https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping

Link to this repository: https://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_mapping/566e456371c6

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_mapping

Type: unrestricted

Revision: 6:566e456371c6

This revision can be installed: True

Times cloned / installed: 670

Name	Description	Version	Minimum Galaxy Version
Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
Filter sequences by mapping View tool metadata	from SAM/BAM file	0.0.8	16.01