Enveomics collection

sam.filter.rb

Filters a SAM or BAM file by target sequences and/or identity.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

• Ruby >= 2.0.

§ Usage

sam.filter.rb --genome in_file --mapping in_file --out-sam out_file [opts]

§ Arguments

Genome*

 --genome in_file  Genome assembly. Supports compression with .gz extension.

Mapping*

 --mapping in_file  Mapping file. Supports compression with .gz extension.

Out sam*

 --out-sam out_file  Output filtered file in SAM format. Supports compression with .gz extension.

G format

 --g-format select  Genome assembly format.

M format

 --m-format select  Mapping file format. SAM supports compression with .gz file extension.

Identity

 --identity float  Set a fixed threshold of percent identity.

No header

 --no-header   Do not include the headers.

Threads

 --threads integer  Threads to use.

Log

 --log out_file  Log file to save output.

Quiet

 --quiet   Run quietly.

* Mandatory.