srf2fasta(1)

✨ srf2fasta ✨

okay bestie, welcome to the srf2fasta page from the Staden io_lib manual, section 1 🎀 she's a lil command-line icon and honestly? she eats. let's get into it 💅

🌸 NAME 🌸

srf2fasta — converts SRF files to fasta format. that's it, that's the whole job, and she does it flawlessly no cap 🦋

💖 SYNOPSIS 💖

srf2fasta [-C] srf_archive

🌈 DESCRIPTION 🌈

so here's the vibe: srf2fasta extracts sequences from an SRF archive and writes them out in fasta format to stdout. like, it takes your archive, pulls the sequences out, and yeets them straight to standard output for you to redirect wherever your heart desires 🫶

fr fr, she writes to stdout, so if you just run her raw you're gonna get a wall of fasta text staring back at you 💀 redirect her, bestie.

✨ OPTIONS ✨

• -C — masks out sequences that are tagged as bad quality. basically she puts a little 🎀 over the questionable ones so they don't show up in your output. protecting your peace, one low-quality read at a time 🙈

🧚 EXAMPLES 🧚

say you wanna extract only the good quality sequences from runX.srf into runX.fasta. the move is:

srf2fasta -C runX.srf > runX.fasta

see how the -C is doing the heavy lifting there? that's the bad-quality mask, and the > is sending it all into your shiny new runX.fasta file. main character energy honestly 👑

👑 AUTHOR 👑

James Bonfield, Wellcome Trust Sanger Institute — ty legend, we love a king who ships good tooling 💜

so yeah, that's the whole page 🦋 go forth, convert your SRFs, mask your bad reads, live your truth ✨ this was the srf2fasta(1) manual from Staden io_lib, dated September 19 — mwah, love u, bye 💅💖