News and Announcements » – Make per-library sff files from ID lists


This script generates per-library sff files using a directory of text files, one per library, which list read ID’s to be included.

The ID list files should contain one read ID per line. If a line contains multiple words (separated by whitespace), then only the first word is used. A ‘>’ character is stripped from the beginning of the line, if present. Blank lines in the file are skipped.

Usage: [options]

Input Arguments:



-i, --input_sff
Input sff file (separate multiple files w/ comma)
-l, --libdir
Directory containing ID list text files, one per library


-p, --sfffile_path
Path to sfffile binary [default: use sfffile in $PATH]
Use external sfffile program instead of equivalent Python routines.
Print debugging output to stdout [default: False]


The result of this script generates sff files for each library.


Make per-library sff files using input.sff and a directory of libs where each file in the directory contains the id lists for each library: -i input.sff -l libs

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