process_sff.py – Convert sff to FASTA and QUAL files

Description:

This script converts a directory of sff files into FASTA, QUAL and flowgram files.

Usage: process_sff.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_dir

Input directory of sff files or a single sff filepath

[OPTIONAL]

--no_trim

Do not trim sequence/qual (requires –use_sfftools option) [default: False]

-f, --make_flowgram

Generate a flowgram file. [default: False]

-t, --convert_to_FLX

Convert Titanium reads to FLX length. [default: False]

--use_sfftools

Use the external programs sfffile and sffinfo for processing, instead of the equivalent python implementation

-o, --output_dir

Input directory of sff files [default: same as input dir]

Output:

This script results in FASTA and QUAL formatted files.

Simple example:

Convert all the sffs in directory “sffs/” to fasta and qual.

process_sff.py -i sffs/

Convert a single sff to fasta and qual.

process_sff.py -i sffs/test.sff

Flowgram example:

Convert all the sffs in directory “sffs/” to fasta and qual, along with a flowgram file.

process_sff.py -i sffs/ -f

Convert a single sff to fasta and qual, along with a flowgram file.

process_sff.py -i sffs/test.sff -f

Output example:

Convert all the sffs in directory “sffs/” to fasta and qual, along with a flowgram file and write them to another directory.

process_sff.py -i sffs/ -f -o output_dir