SSW-ALIGN(1)

📦
version 1.1 · 5 versions
, in debian bookworm, ubuntu jammy

✨ SSW-ALIGN(1) ✨

okay bestie, gather round, because this is ssw-align from section 1 of the manual — User Commands, the cool kids' section — and it is literally a fast Smith-Waterman aligner 🧬💅

🎀 NAME 🎀

ssw-align — a fast Smith-Waterman aligner. no cap, that's the whole name, that's the whole vibe. ✨

🦋 SYNOPSIS 🦋

ssw-align [options] ... <target.fasta> <query.fasta>(or <query.fastq>)

yes babe, the target file first, then the query file, and the query can be either .fasta or .fastq. the ... is just sitting there being mysterious. 🙈

💖 DESCRIPTION 💖

so this little command line tool uses SSW, which is a fast SIMD optimized alignment library, to do alignments on your input files. it's giving optimized. it's giving SIMD. it's giving slay. ⚡

your input files can be in FASTA or FASTQ format, and both the target and the query file can hold multiple sequences. here's the tea though, and you're gonna wanna hear this one: every single sequence in the query file gets aligned with every single sequence in the target file. all of them. no skipping. so if your target file has N sequences and your query file has M sequences, you're gonna end up with M*N alignments. that's just math, bestie. 🍓

🌸 OPTIONS 🌸

  • -m N — N is a positive integer, and it's the weight for a match in genome sequence alignment. default? 2. 💖
  • -x N — N is a positive integer, and -N gets used as the weight for a mismatch in genome sequence alignment. default is 2 as well. ✨
  • -o N — N is a positive integer, and -N is the weight for gap opening. default: 3. 🎀
  • -e N — N is a positive integer, and -N is the weight for gap extension. default: 1. 🦋
  • -p — do protein sequence alignment. without this option, ssw_test will do genome sequence alignment instead. so like, if it's protein, say it's protein. 💅
  • -a FILE — FILE is either the Blosum or Pam weight matrix. default: Blosum50. 🌈
  • -c — return the alignment path. 🛣️
  • -f N — N is a positive integer. only output the alignments with the Smith-Waterman score >= N. filter that timeline, bestie. ⭐
  • -r — the best alignment gets picked between the original read alignment and the reverse complement read alignment. main character energy only. 👑
  • -s — output in SAM format. default is no header. 📄
  • -h — if -s is used, include the header in the SAM output. 🫶

🧚 OUTPUT FORMATS 🧚

the software can output SAM format or BLAST like format results. if you want the full spec of SAM format, go look at:

http://samtools.sourceforge.net/SAM1.pdf

also! the additional optional field "ZS" tells you the suboptimal alignment score. iykyk. 🔥

heads up bestie: that link is the official SAM spec, so if the format stuff confuses you, that PDF is the source of truth, not me. 💀

and that's the page, babe. it's from ssw-align, dated February 2021, and honestly? iconic. periodt. 💜🌸

📦 where this page comes from