SCYTHE(1)

💅 SCYTHE — the Bayesian adaptor trimmer (yes, like the reaper, but for adaptors)

okay bestie, listen. You know how your reads come back from the sequencer with a little... extra? Some adaptor sequence clinging to the 3´ end like a situationship that won't leave? That's literally what scythe is for. It's a Bayesian adaptor trimmer, and it's here to cut that nonsense off. 🌾✨

✨ NAME ✨

scythe — Bayesian adaptor trimmer. That's the whole vibe. 🎀

🌸 SYNOPSIS 🌸

scythe -t sanger -a /path/to/adaptors.fasta [options]
<sequences.fastq.gz>

Trim 3´-end adaptor contaminants off sequence files. If no output file is specified, scythe will use stdout.

no cap, if you don't tell it where to put the output, it just yeets everything straight to stdout. plan accordingly, bestie. 💖

👑 OPTIONS 👑

• -p, --prior prior — the prior (default: 0.300)
• -q, --quality-type quality type — pick your encoding: either illumina, solexa, or sanger (default: sanger)
• -m, --matches-file matches file — the matches file (default: no output)
• -o, --output-file output trimmed sequences file — where the trimmed sequences go (default: stdout)
• -t, --tag — add a tag to the header indicating Scythe cut a sequence (default: off)
• -n, --min-match — smallest contaminant to consider (default: 5)
• -M, --min-keep — filter sequences less than or equal to this length (default: 35)
• --quiet — don´t output statistics about trimming to stdout (default: off)
• --help — display this help and exit
• --version — output version information and exit

🦋 the quality encoding schemes, aka the lore

These are the quality encoding schemes scythe recognises (see --quality):

• phred — PHRED quality scores (e.g. from Roche 454). ASCII with no offset, range: [4, 60].
• sanger — Sanger are PHRED ASCII qualities with an offset of 33, range: [0, 93]. From NCBI SRA, or Illumina pipeline 1.8+.
• solexa — Solexa (also very early Illumina — pipeline < 1.3). ASCII offset of 64, range: [-5, 62]. Uses a different quality-to-probabilities conversion than other schemes.
• illumina — Illumina output from pipeline versions between 1.3 and 1.7. ASCII offset of 64, range: [0, 62].

the solexa one is out here doing its own little conversion dance that nobody else does. it's giving main character energy, but also please pay attention to it. 🙈

🧚 FILES 🧚

adaptors.fasta: Provide contaminant sequences as a fasta-formatted file. See /usr/share/doc/scythe/illumina_adaptors.fa.

N.B.: Index/Barcode sequences should be substituted for Ns in the example adaptor file.

like, literally swap those Ns out for your actual index/barcode sequences, bestie. don't skip that part. 💀

⭐ AUTHOR ⭐

Vince Buffalo, https://github.com/vsbuffalo

and that's the whole page, fr fr. shoutout to Vince Buffalo for writing this one — this is the scythe manual, version dated May 2015, page SCYTHE(1). slay, go trim some adaptors, periodt. 💅🌾💖