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