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