GUSTAF(1)

📦
version 2.5.2 · 2 versions
, in ubuntu stonking

🦋 NAME 🦋

gustaf — Gustaf — Generic mUlti-SpliT Alignment Finder: the tool for split-read mapping that allows multiple splits. bestie, it's literally right there in the acronym 💅

🎀 SYNOPSIS 🎀

gustaf [OPTIONS] <GENOME FASTA FILE> <READ FASTA FILE>

gustaf [OPTIONS] <GENOME FASTA FILE> <READ FASTA FILE> <READ FASTA FILE 2>

🌸 DESCRIPTION 🌸

okay so, the whole vibe here: GUSTAF uses SeqAns STELLAR to find splits as local matches on different strands or chromosomes. iconic. ✨

And because chaining matches is like, a whole personality, you can specify the criteria and penalties to chain these matches. The output file contains the breakpoints along the best chain. 👑

The genome file is used as database input, the read file as query input. one's the reference, one's the question, they're in their lane fr fr.

All STELLAR options are supported. See STELLAR documentation for STELLAR parameters and options. go ask STELLAR about STELLAR's own business, not me 🫶

(c) 2011-2026 by Kathrin Trappe 💜

👑 REQUIRED ARGUMENTS 👑

  • FASTA_FILE_1 INPUT_FILE — Valid filetypes are: .fq, .fastq, .fasta, and .fa.
  • FASTA_FILE_2 List of INPUT_FILE's — Either one (single-end) or two (paired-end) read files. Valid filetypes are: .fq, .fastq, .fasta, and .fa. so like, one file = single-end, two files = paired-end, you get to choose your destiny 🦋

🔥 OPTIONS 🔥

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

💖 Main Options 💖

  • -tp, --transPen INTEGER — Interchromosomal translocation penalty. Default: 5.
  • -ip, --invPen INTEGER — Inversion penalty. Default: 5.
  • -op, --orderPen INTEGER — Intrachromosomal order change penalty. Default: 0.
  • -oth, --overlapThresh DOUBLE — Allowed overlap between matches. Default: 0.5.
  • -gth, --gapThresh INTEGER — Allowed gap length between matches; default value corresponse to expected size of microindels (5 bp). Default: 5.
  • -ith, --initGapThresh INTEGER — Allowed initial or ending gap length at begin and end of read with no breakpoint (e.g. due to sequencing errors at the end). Default: 15.
  • -bth, --breakendThresh INTEGER — Allowed initial or ending gap length at begin and end of read that creates a breakend/breakpoint (e.g. for reads extending into insertions). Default: 30.
  • -tth, --tandemThresh INTEGER — Minimal length of (small) insertion/duplication with double overlap to be considered tandem repeat. Default: 50.
  • -pth, --breakpoint-pos-range INTEGER — Allowed difference in breakpoint position. Default: 5.
  • -cbp, --complex-breakpoints — Disable inferring complex SVs. (yes the flag does the off thing, that's on purpose 🙈)
  • -st, --support INTEGER — Number of supporting reads. Default: 2.
  • -mst, --mate-support INTEGER — Number of supporting concordant mates. Default: 2.
  • -ll, --library-size INTEGER — Library size of paired-end reads.
  • -le, --library-error INTEGER — Library error (sd) of paired-end reads.
  • -rc, --revcompl — Disable reverse complementing second mate pair input file.

🌈 Input Options 🌈

  • -m, --matchfile INPUT_FILE — File of (stellar) matches. Valid filetypes are: .gff and .GFF.

✨ Output Options ✨

  • -gff, --gffOut OUTPUT_FILE — Name of gff breakpoint output file. Valid filetypes are: .txt and .gff. Default: breakpoints.gff.
  • -vcf, --vcfOut OUTPUT_FILE — Name of vcf breakpoint output file. Valid filetypes are: .vcf and .txt. Default: breakpoints.vcf.
  • -j, --jobName STRING — Job/Queue name. Default: .
  • -do, --dots — Enable graph output in dot format. 🕸️

🚀 Parallelization Options 🚀

  • -nth, --numThreads INTEGER — Number of threads for parallelization of I/O. Default: 1.

💖 Main Options 💖

(yes bestie, it says Main Options again — that's exactly how it is in here, we don't question it, we respect it 🫶)

  • -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. (chatty era 💬)

🍓 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.
💀 quick reminder bestie: those range limits are not suggestions, they're the law of the land. go outside the range and that's on you, no cap.

and that's the whole page, my love 🫶 this is gustaf version 1.0.0, dated August 2014 — yes it's older than some of us and it's still serving, we love a vintage icon 👑✨

📦 where this page comes from