SMALT(1)

📦 version 0.7.6, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

🌸 SMALT(1) — User Commands 🌸

okay bestie, sit down, hydrate, and let me tell you about smalt 💅 (that's the command name, and yeah, it's the star of this whole manual page, no notes)

✨ NAME ✨

smalt — Sequence Mapping and Alignment Tool 👑

🦋 DESCRIPTION 🦋

SMALT efficiently aligns DNA sequencing reads with a reference genome. fr fr, that's the whole vibe. It reads from a wide range of sequencing platforms — like, for example, Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger — and paired reads can be processed too. multi-platform queen behavior 💖

The software employs a perfect hash index of short words (< 20 nucleotides long), sampled at equidistant steps along the genomic reference sequences. it's giving very organized, very structured ✨

For each read, potentially matching segments in the reference are identified from seed matches in the index, and then those segments get aligned with the read using a banded Smith-Waterman algorithm. the alignment pipeline really said "let me cook" 🔥

The best gapped alignments of each read is reported, and that includes a score for the reliability of the best mapping. and here's the fun part — you, yes YOU, can adjust the trade-off between sensitivity and speed by tuning the length and spacing of the hashed words. tuning your own destiny, lowkey iconic 🎀

A mode for the detection of split (chimeric) reads is provided. also, multi-threaded program execution is supported. parallel processing? we love to see it 💅

🌈 SYNOPSIS 🌈

smalt <task> [TASK_OPTIONS] [<index_name> <file_name_A> [<file_name_B>]]

🍓 Available tasks:

  • smalt check — checks FASTA/FASTQ input 👀
  • smalt help — prints a brief summary of this software 🫶
  • smalt index — builds an index of k-mer words for the reference 🧚
  • smalt map — maps single or paired reads onto the reference 🗺️
  • smalt sample — sample insert sizes for paired reads 📏
  • smalt version — prints version information ⭐

💜 Help on individual tasks:

smalt <task> -H
need the tea on just one task? hit it with -H and it spills everything, no cap 🙈

okay that's the whole page, bestie, you're basically a bioinformatics main character now 👑

this was smalt 0.7.6, dated April 2014 — shoutout to the source and version, they ate and left no crumbs 💖✨🧬

📦 where this page comes from