GT-HOP(1)

📦
version 1.6.6 · 5 versions
, in ubuntu resolute, ubuntu stonking

🦋 GT-HOP(1) — the GenomeTools manual, but make it cute 🦋

okay bestie, welcome to the GenomeTools Manual page for gt-hop. pull up a chair, grab a strawberry 🍓, and let's get into it. this is the cognate sequence-based homopolymer error correction tool and she is lowkey a whole vibe.

✨ NAME ✨

gt-hop — cognate sequence-based homopolymer error correction.

like, that's her whole thing. no cap. 💅

🌸 SYNOPSIS 🌸

gt hop -<mode> -c <encseq> -map <sam/bam> -reads <fastq> [options...]

that's the shape of it, bestie. <mode> goes in, the encseq goes in, the mapping goes in, the reads go in, and out comes corrected goodness. 🫶

💖 DESCRIPTION 💖

okay so here are ALL the options, and I mean all of them, no skips, no shortcuts, periodt.

  • -c [string] — the cognate sequence. she has to be encoded, using gt encseq encode. that's the rules. 🎀
  • -map [string] — the mapping of reads to the cognate sequence. it MUST be in SAM/BAM format, and it MUST be sorted by coordinate. you can prep that up e.g. using samtools sort. sorting is not optional, bestie. 😭
  • -sam [yes|no] — tells it the mapping file is SAM. default: BAM. so if you say nothing, she assumes BAM, and if you actually handed her SAM, that's a you problem. 💀
  • -aggressive [yes|no] — correct as much as possible. she's going for it. 🔥
  • -moderate [yes|no] — mediate between sensitivity and precision. the middle child, the peacekeeper. 🧚
  • -conservative [yes|no] — correct only most likely errors. cautious queen. 👑
  • -expert [yes|no] — manually select correction criteria. you're driving now. no pressure. 🙈
  • -reads — uncorrected read file(s) in FastQ format. the corrected reads get output in the current working directory in files named just like the input files, each with a prefix prepended (see the -outprefix option). also: -reads lets you output the reads in the same order as in the input, and it is mandatory if the SAM contains more than a single primary alignment for each read (e.g. output of bwasw). see also the -o option as an alternative. 🌈
  • -outprefix [string] — prefix for output filenames (corrected reads). when -reads is specified, the prefix is prepended to each input filename. default: hop_ 🎀
  • -o [string] — output file for corrected reads (see also -reads/-outprefix). if -o is used, reads are output in a single file, in the order they are found in the SAM file — which usually differs from the original order, jsyk. and this will only work if the reads were aligned with software that includes only 1 alignment for each read (e.g. bwa). default: undefined. ⭐
  • -hmin [value] — minimal homopolymer length in the cognate sequence. default: 3 ✨
  • -read-hmin [value] — minimal homopolymer length in reads. default: 2 ✨
  • -qmax [value] — maximal average quality of homopolymer in a read. default: 120 ✨
  • -altmax [value] — max support of alternate homopol. length. e.g. 0.8 means: do not correct any read if the homop. length in more than 80%% of the reads has the same value, different from the cognate. if altmax is set to 1.0, reads are always corrected. default: 0.800000 💅
  • -cogmin [value] — min support of cognate sequence homopol. length. e.g. 0.1 means: do not correct any read if the cognate homop. length is not present in at least 10%% of the reads. if cogmin is set to 0.0, reads are always corrected. 🦋
  • -mapqmin [value] — minimal mapping quality. default: 21 🌸
  • -covmin [value] — minimal coverage. e.g. 5 means: do not correct any read if coverage (number of reads mapped over the whole homopolymer) is less than 5. if covmin is set to 1, reads are always corrected. default: 1 🌸
  • -allow-muliple [yes|no] — allow multiple corrections in a read. default: no. (and yes, the option is spelled exactly like that, I'm not touching it, that's canon 💀)
  • -clenmax [value] — maximal correction length. default: unlimited. 🌀
  • -ann [string] — annotation of the cognate sequence. it must be sorted by coordinates on the cognate sequence (this can be done e.g. using gt gff3 -sort). if -ann is used, corrections will be limited to homopolymers starting or ending inside the feature type indicated by the -ft option. format: sorted GFF3. default: undefined. 📍
  • -ft [string] — feature type to use when the -ann option is specified. default: CDS 💜
  • -v [yes|no] — be verbose. default: no. (turn it on if you want her to yap, we love a yapper 🗣️)
  • -help — display help for basic options and exit. 🚪
  • -help+ — display help for all options and exit. 🚪✨
  • -version — display version information and exit. 🚪🎀

💫 Correction mode 💫

okay this part matters, bestie. one of the options -aggressive, -moderate, -conservative or -expert MUST be selected. like, you have to pick one. no waffling.

the -aggressive, -moderate and -conservative modes are presets of the criteria by which it is decided if an observed discrepancy in homopolymer length between the cognate sequence and a read shall be corrected or not. a description of the single criteria is provided by using the -help+ option. the presets are equivalent to the following settings:

  • -hmin — -aggressive: 3, -moderate: 3, -conservative: 3
  • -read-hmin — -aggressive: 1, -moderate: 1, -conservative: 2
  • -altmax — -aggressive: 1.00, -moderate: 0.99, -conservative: 0.80
  • -refmin — -aggressive: 0.00, -moderate: 0.00, -conservative: 0.10
  • -mapqmin — -aggressive: 0, -moderate: 10, -conservative: 21
  • -covmin — -aggressive: 1, -moderate: 1, -conservative: 1
  • -clenmax — -aggressive: unlimited, -moderate: unlimited, -conservative: unlimited
  • -allow-multiple — -aggressive: yes, -moderate: yes, -conservative: no

(and that's -refmin right there in the presets, exactly as written, iykyk — I'm not the one who named it, I'm just the messenger 🫡)

the aggressive mode tries to maximize the sensitivity, the conservative mode tries to minimize the false positives. an even more conservative set of corrections can be achieved using the -ann option (see -help+).

the -expert mode allows one to manually set each parameter; the default values are the same as in the -conservative mode. main character energy, honestly. 👑

finally — and this is for evaluation purposes only, so don't get any ideas — the -state-of-truth mode can be used: this mode assumes that the sequenced genome has been specified as cognate sequence and outputs an ideal list of corrections. it's giving lab-notebook fantasy, and it's iconic. 🌟

😭 REPORTING BUGS 😭

found a bug? report it to https://github.com/genometools/genometools/issues. don't be shy, they want to know, fr fr. 🐛

that's the whole page, bestie. 💖 this was GenomeTools 1.6.6, dated 11/09/2025, page GT-HOP(1) — mwah, slay, go correct some homopolymers. 🎀✨💅

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