srf2fastq(1)

✨ srf2fastq — bestie, let's turn those SRF archives into fastq 💅

okay so real talk, this is srf2fastq from the Staden io_lib girlies, and it's literally the glow-up machine for your sequence data. she's a manual page, she's a vibe, she's here to help.

🌸 NAME 🌸

srf2fastq — converts SRF files to Sanger fastq format. that's it, that's the whole job, and she does it iconically. 💖

🎀 SYNOPSIS 🎀

srf2fastq [options] srf_archive ...

🦋 DESCRIPTION 🦋

so srf2fastq extracts sequences and qualities from one or more SRF archives and writes them out in Sanger fastq format to stdout. no cap, that's the whole plot. ✨

lowkey important tho: Illumina also has a fastq format of their own (the one used in the GERALD directories) and it differs slightly — it uses log-odds scores for the quality values. the format described here is the traditional Phred style of quality encoding. so don't get it twisted, bestie. 🙈

💅 OPTIONS 💅

• -c — outputs calibrated confidence values using the ZTR CNF1 chunk type, giving you a single quality per base. without this, she uses the original Illumina _prb.txt files instead — those ones have four quality values per base, stored in the ZTR CNF4 chunks.
• -C — masks out sequences tagged as bad quality. bye bye garbage reads, we don't know her. 🚮
• -s root — generates files on disk with filenames starting with root, one file per non-explicit element in the SRF/ZTR region (REGN) chunk. typically that gives you two files for paired end runs. the filename suffixes come from the names listed in the SRF region chunks. ⚠️ this option conflicts with the -S parameter.
• -S — splits sequences into regions, but sequentially lists each sequence region to stdout instead of splitting them into separate files on disk. ⚠️ this option conflicts with the -s parameter.
• -n — when you're using -s, the filename suffixes are just simply numbered (starting with 1) instead of using the names listed in the SRF region chunks. simplicity slay. ✨
• -a — appends the region index to the sequence names. like, it generates "name/1" and "name/2" for a paired read. cute, organized, obsessed. 🫶
• -e — include any explicit sequence (ZTR region chunk of type 'E') in the sequence output. the explicit sequence also gets included in the quality line too. currently this is utilised by ABI SOLiD to store the last base of the primer. iykyk. 💜
• -r region list — reverse complements the sequence and reverses the quality values for all regions in the region list. it's a comma separated list of integer values enumerating the regions, starting from 1. ⚠️ heads up bestie: this option only works when either -s or -S are specified. don't come crying to me if you forget. 😭

🔥 EXAMPLES 🔥

1. to extract only the good quality sequences from all srf files in the current directory, using calibrated confidence values (if available):

srf2fastq -c -C *.srf > runX.fastq

2. to extract a paired end run into two separate files, with sequences named name/1 and name/2:

srf2fastq -s runX -a -n runX.srf

3. to extract a paired end run as a single file, alternating forward and reverse sequences, with the second read being reverse complemented:

srf2fastq -S -r 2 runX.srf > runX.fastq

👑 AUTHOR 👑

James Bonfield, Steven Leonard — Wellcome Trust Sanger Institute. absolute legends, fr fr. 🫡

okay that's the whole page bestie, go forth and convert. ✨💖

srf2fastq(1) · Staden io_lib · December 10 — mwah, written by the Sanger girlies, dated December 10, version vibes from Staden io_lib. periodt. 💅🌸