News and Announcements » – Trim sff primers


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

Usage: [options]

Input Arguments:



-l, --libdir
The directory containing per-library sff files
-m, --input_map
Path to the input mapping file describing the libraries


-p, --sfffile_path
Path to sfffile binary [default: sfffile]
-q, --sffinfo_path
Path to sffinfo binary [default: sffinfo]
Use external sffinfo and sfffile programs instead of equivalent Python implementation.
Print command-line output for debugging [default: False]


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. -l sff_dir/ -m input_map.txt