STELLAR(1)

📦
version 2.5.2 · 2 versions
, in ubuntu stonking

💖 STELLAR 💖

okay bestie, listen. the tool is stellar, and it stands for the SwifT Exact LocaL AligneR — yes the capital letters are doing a whole thing, it's giving acronym, it's iconic, we love her 💅

Manual section: STELLAR(1). Pull up a chair. 🎀

✨ SYNOPSIS ✨

stellar [OPTIONS] <FASTA FILE 1> <FASTA FILE 2>

🦋 DESCRIPTION 🦋

so here's the tea, fr fr: STELLAR implements the SWIFT filter algorithm (Rasmussen et al., 2006) plus a verification step for the SWIFT hits, and that verification step applies local alignment, gapped X-drop extension, and extraction of the longest epsilon-match. like, it filters first and then it actually checks, bestie. main character behavior only. 👑

what you feed it is two files, each one holding one or more sequences in FASTA format. every sequence from file 1 gets compared to every sequence in file 2. and listen — the sequences in file 1 are used as the database, the sequences in file 2 are used as the queries. don't mix them up, i'm begging 🫶

copyright, no cap: (c) 2010-2026 by Birte Kehr

🌸 REQUIRED ARGUMENTS 🌸

  • FASTA_FILE_1 INPUT_FILE — your first input file, and the valid filetypes are: .fasta and .fa.
  • FASTA_FILE_2 INPUT_FILE — your second input file, and the valid filetypes are: .fasta and .fa.

⭐ OPTIONS ⭐

  • -h, --help — Display the help message.
  • --version — Display version information.

💜 Main Options:

  • -e, --epsilon DOUBLE — Maximal error rate (max 0.25). In range [0.0000001..0.25]. Default: 0.05.
  • -l, --minLength INTEGER — Minimal length of epsilon-matches. In range [0..inf]. Default: 100.
  • -f, --forward — Search only in forward strand of database.
  • -r, --reverse — Search only in reverse complement of database.
  • -a, --alphabet STRING — Alphabet type of input sequences (dna, rna, dna5, rna5, protein, char). One of dna, dna5, rna, rna5, protein, and char.
  • -v, --verbose — Set verbosity mode.
not you needing a whole alphabet crisis in the middle of an alignment. pick one of the six and go, bestie 💀

🍓 Filtering Options:

  • -k, --kmer INTEGER — Length of the q-grams (max 32). In range [1..32].
  • -rp, --repeatPeriod INTEGER — Maximal period of low complexity repeats to be filtered. Default: 1.
  • -rl, --repeatLength INTEGER — Minimal length of low complexity repeats to be filtered. Default: 1000.
  • -c, --abundanceCut DOUBLE — k-mer overabundance cut ratio. In range [0..1]. Default: 1.

🌈 Verification Options:

  • -x, --xDrop DOUBLE — Maximal x-drop for extension. Default: 5.
  • -vs, --verification STRING — Verification strategy: exact or bestLocal or bandedGlobal. One of exact, bestLocal, and bandedGlobal. Default: exact.
  • -dt, --disableThresh INTEGER — Maximal number of verified matches before disabling verification for one query sequence (default infinity). In range [0..inf].
  • -n, --numMatches INTEGER — Maximal number of kept matches per query and database. If STELLAR finds more matches, only the longest ones are kept. Default: 50.
  • -s, --sortThresh INTEGER — Number of matches triggering removal of duplicates. Choose a smaller value for saving space. Default: 500.

🎀 Output Options:

  • -o, --out OUTPUT_FILE — Name of output file. Valid filetypes are: .txt and .gff. Default: stellar.gff.
  • -od, --outDisabled OUTPUT_FILE — Name of output file for disabled query sequences. Valid filetypes are: .sam[.*], .raw[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .fas[.*], .faa[.*], .fa[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression. Default: stellar.disabled.fasta.
that extension list is LONG and she earned it. type it, don't guess it, iykyk ✨

📚 REFERENCES 📚

Kehr, B., Weese, D., Reinert, K.: STELLAR: fast and exact local alignments. BMC Bioinformatics, 12(Suppl 9):S15, 2011.

and that's the whole vibe check, bestie 💖 this page is stellar version 1.4.15 (tarball build), manual section STELLAR(1). go align something gorgeous ✨🦋👑

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