Split FASTQ file to FASTA and QUAL files

Description

Given a FASTQ file, extracts sequences to FASTA file and base qualities to QUAL file. Provides also summary information on the sequences.

Parameters

Details

In addition to FASTA and QUAL files, this tool provides summary statistics on sequence length, number of ambiguous bases, and homopolymer length.

This tool is based on the Fastq.info command of the Mothur package.

Output

The analysis output consists of the following:

• reads.fasta: Sequences
• basequalities.qual: Base quality values for the sequences
• summary.tsv: Summary statistics for all the sequences

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.