SEQTK(1)

💖 SEQTK(1) 💖

okay bestie, sit down, because this one is a whole vibe. this is the manual page for seqtk, and she's a little Swiss Army knife for FASTA/Q files. no cap.

✨ NAME ✨

seqtk — sampling, trimming, fastq2fasta, subsequence, reverse complement 🦋

🌸 SYNOPSIS 🌸

seqtk <command> <arguments>

like, you give her a command and then the arguments for it. that's the whole thing. she's not complicated, she's just booked and busy.

🎀 DESCRIPTION 🎀

So rn, seqtk supports quality-based trimming with the phred algorithm, converting fastq to fasta, reverse complementing sequences, extracting or masking subsequences in regions given in a BED/name list file, and more. the "and more" is doing a lot of heavy lifting there but periodt 💅

She also has a subsampling module, so you can sample exactly n sequences, or just a fraction of sequences. exact n. not vibes-based. precise. main character energy. 👑

And the best part: seqtk supports both fasta and fastq input files, which can be optionally gzip compressed. so compressed or not, she eats either one. 🍓

🫶 COMMANDS 🫶

okay so here's the menu, and yes you have to pick one. no, you can't just run her naked. 🙈

• seq — common transformation of FASTA/Q ✨
• comp — get the nucleotide composition of FASTA/Q
• sample — subsample sequences
• subseq — extract subsequences from FASTA/Q
• trimfq — trim FASTQ using the Phred algorithm
• hety — regional heterozygosity
• mutfa — point mutate FASTA at specified positions
• mergefa — merge two FASTA/Q files
• randbase — choose a random base from hets
• cutN — cut sequence at long N
• listhet — extract the position of each het

okay that's the whole page, you're basically a seqtk girlie now 💜 go forth and transform some sequences.

this has been seqtk 1.0, February 2014, signing off 🎀 bye bestie, mwah 💖