## Metagenomics / Extract sequences from a SFF file

### Description

Extract a FASTA sequence file and a QUAL quality file from a SFF file.

### Parameters

- Trim reads for quality (yes, no) [no]

### Details

Extract a FASTA sequence file and a QUAL quality file from a SFF file. Sequences can optionally be trimmed for quality.

This tool is based on the Mothur package.

### Output

The analysis output consists of the following if Trim option is selected:

- reads.fasta: Extracted trimmed reads in FASTA format
- reads.qual: Extracted trimmed quality values in QUAL format

The analysis output consists of the following if Trim option is not selected:

- reads.raw.fasta: Extracted raw reads in FASTA format
- reads.raw.qual: Extracted raw quality values in QUAL format

### References

Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.