GOBY(1)

🌸 GOBY(1) — the goby page, but make it make sense 🌸

okay bestie, welcome to GOBY(1), straight out of the General Commands Manual. She's a whole tool for wrangling sequencing data, and we're gonna go through the ENTIRE thing, no skipping, no skimming, periodt. 💅

✨ NAME ✨

goby — sequencing data and results analysis tool

🦋 SYNOPSIS 🦋

goby <mem> <mode> [OPTIONS]

💖 DESCRIPTION 💖

Goby provides facilities to manage sequencing data and ease the implementation of data analysis pipelines. that's the whole vibe, she's a pipeline girlie. 🫶

🎀 MANDATORY INFORMATION 🎀

no skipping these two, they're the mandatory ones, the main characters. 👑

• <mem> — the human-readable amount of memory you're handing to Goby. like literally human readable, so it could be 1m, 145m, 3g, ... you get the idea. 🧠
• <mode> — this tells Goby which mode <mode> to run in. and <mode> has to be one of these (you can use the long name OR the short name that's chillin' inside the parentheses):
• aggregate-by-peak-distance (abpd)
• aggregate-by-peak-rpkm-difference (abprd)
• alignment-to-annotation-counts (atac)
• alignment-to-counts (altc)
• alignment-to-pileup (atp)
• alignment-to-read-set (atrs)
• alignment-to-text (att)
• alignment-to-transcript-counts (attc)
• annotation-penalty (ap)
• annotations-to-counts (antc)
• barcode-decoder (bd)
• base-stats (bs)
• bisulfite-conversion (bc)
• build-sequence-cache (bsc)
• compact-file-stats (cfs)
• compact-to-fasta (ctf)
• compact-to-sam (cts)
• compare-alignment-to-genome (catg)
• concatenate-alignments (ca)
• concatenate-compact-reads (ccr)
• count-archive-to-peak-annotations (catpa)
• count-archive-to-peak-union-annotations (catpua)
• counts-to-bedgraph (ctb)
• counts-to-wiggle (ctw)
• coverage (c)
• diff-alignments (da)
• discover-sequence-variants
• display-sequence-variations
• empirical-p (ep)
• extract-splicing-events (ese)
• fasta-to-compact (ftc)
• fdr (f)
• files-to-attributes (fta)
• heptamer-weights (hw)
• infer-sex (hasResult)
• last-to-compact (ltc)
• merge-compact-alignments (mca)
• methyl-stats (ms)
• read-quality-stats (rqs)
• reads-to-weights (rtw)
• reformat-compact-reads (rcr)
• run-parallel (rp)
• sam-comparison (sc)
• sam-extract-reads (ser)
• sam-to-compact (stc)
• sam-to-compact-old (stco)
• sam-to-compact-samhelper (stcs)
• sample-quality-scores (sqs)
• sequence-variation-stats (svs)
• sequence-variation-stats2 (svs2)
• set-to-text (stt)
• simulate-reads (sr)
• sort (s)
• sort-1 (s1)
• split-compact-reads (scr)
• split-fasta (sf)
• split-transcripts (st)
• stats
• suggest-position-slices (sps)
• tab-to-column-info (ttci)
• tally-bases (tb)
• tally-reads (tr)
• test-r-connection (trc)
• trim (t)
• upgrade (u)
• vcf-compare (vc)
• vcf-subset (vs)
• vcf-to-genotype-map (vtgm)
• vcf-to-indel-set (vtis)
• vcf-to-tab (vtt)
• version (v)
• within-group-variability (wgv)

heads up: notice discover-sequence-variants, display-sequence-variations and stats are out here with no short name in parentheses. they're just like that. iconic of them honestly. 💅

🌈 OPTIONS 🌈

mode-specific-options

each of the above modes has its own specific options, they're all unique little snowflakes. 🧚 the complete list of options for a given mode <mode> can be get by running

goby 100m <mode>

which returns a complete list of options for running the mode <mode>, plus a description of what this mode provides. so yeah, that's your cheat code. 🔥

• -h, --help — displays usage help information
• -H, --x-help — displays help for dynamic options

👑 AUTHOR 👑

this manual page was written by Pierre Gruet <pgt@debian.org> from the Debian project, but may be used by others. shoutout to Pierre, we love a Debian bestie. 🫶

aaaaand that's the whole page bestie, you ate it. 💖 no notes. the source is GOBY(1) and the date on this one is 08-08-2021 — so yes she's an August 8th, 2021 girlie. 🌸✨ go forth and sequence. 🦋