SUMATRA(1)

✨ SUMATRA ✨

okay so bestie, welcome to sumatra(1) — the user command that does fast and exact comparison and clustering of sequences 🧬💅 like, it's literally right there in the name section, and I'm not gonna gatekeep it from you.

🌸 SYNOPSIS 🌸

sumatra [options] <dataset1> [dataset2]

that's it. that's the whole vibe. options, then one dataset, then maybe a second one if you're feeling extra 🫶

💖 DESCRIPTION 💖

so what does she actually do? Sumatra computes all the pairwise LCS (Longest Common Subsequence) scores of one nucleotide dataset, or between two nucleotide datasets. all of them. every pair. she's thorough like that 👑

✨ OPTIONS ✨

• -h — [H]elp, bestie. prints <this> help. iconic behaviour honestly 🎀
• -l — the reference sequence length is the shortest one.
• -L — the reference sequence length is the largest one. big main character energy 💅
• -a — the reference sequence length is the alignment length (this is the default, so if you do nothing, this is what you get).
• -n — the score gets normalized by the reference sequence length (also default). she likes things tidy ✨
• -r — raw score, not normalized. no glow-up, just the numbers as they are.
• -d — the score is expressed as a distance (default is: score expressed as similarity). lowkey a whole different lens on the same data 🔍
• -t ##.## — score threshold, and okay this one has layers, so stay with me:
  • if the score is normalized and expressed in similarity (that's the default), then it's an identity — so like 0.95 means an identity of 95%.
  • if the score is normalized and expressed in distance, then it's (1.0 - identity) — so like 0.05 means an identity of 95%. math girlie behaviour, we love her 💜
  • if the score is not normalized and expressed in similarity, then it's the length of the Longest Common Subsequence.
  • if the score is not normalized and expressed in distance, then it's (reference length - LCS length).

only sequence pairs with a similarity above ##.## get printed, so it's giving very exclusive guest list 🚫✋

Default: 0.00 (which means no threshold at all — everyone's invited).

• -p ## — number of threads used for computation (default=1). multitasking queen 🧚
• -g — n's are replaced with a's (default: sequences with n's are discarded — bye bye 👋).
• -x — adds four extra columns with the count and length of both sequences. more data, more slay 📊
• dataset1 — (first argument) the nucleotide dataset to analyze.
• dataset2 — (second argument) optionally, the second nucleotide dataset.

🌈 RESULTS 🌈

here's your results table decoder ring, because the columns are just numbers until someone tells you what they mean:

• column 1 : Identifier sequence 1
• column 2 : Identifier sequence 2
• column 3 : Score
• column 4 : Count of sequence 1 (only with option -x)
• column 5 : Count of sequence 2 (only with option -x)
• column 6 : Length of sequence 1 (only with option -x)
• column 7 : Length of sequence 2 (only with option -x)

so like, columns 4 through 7 are the -x exclusives. they don't show up unless you ask for them. no cap 🙈

🦋 SEE ALSO 🦋

• http://metabarcoding.org/sumatra

go read it, iykyk ⭐

and that's the whole page, bestie 💖 this was sumatra 1.0.03, from August 2015, living in section 1 of the manual. she's an elder but she still ate. periodt 👑🌸