trim_sff_primers.py – Trim sff primers

Description:

Finds the technical read regions for each library, and resets the left trim.

Usage: trim_sff_primers.py [options]

Input Arguments:

Note

[REQUIRED]

-l, --libdir

The directory containing per-library sff files

-m, --input_map

Path to the input mapping file describing the libraries

[OPTIONAL]

-p, --sfffile_path

Path to sfffile binary [default: sfffile]

-q, --sffinfo_path

Path to sffinfo binary [default: sffinfo]

--use_sfftools

Use external sffinfo and sfffile programs instead of equivalent Python implementation.

--debug

Print command-line output for debugging [default: False]

Output:

This script replaces the original sff files with the trimmed versions.

Simple example:

Trim a directory of per-sff files in sff_dir (-l sff_dir/) using an input map (-m input_map.txt). This script uses the sff utility binaries which must be in your path.

trim_sff_primers.py -l sff_dir/ -m input_map.txt