--- name: "goby" section: "1" platform: "linux" package: "goby-java" version: "3.3.1+dfsg2-11" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/goby" --- # goby(1) Sequencing data and results analysis tool ## NAME goby - Sequencing data and results analysis tool ## SYNOPSIS **goby \ \ \[*OPTIONS*\]** ## DESCRIPTION **Goby** provides facilities to manage sequencing data and ease the implementation of data analysis pipelines. ## MANDATORY INFORMATION - **\** Human-readable amount of memory to allocate to **Goby** e.g. could be 1m, 145m, 3g, ... - **\** Indicates to use the mode \ of **Goby** when running. \ must be one of the following ones (either the long name or the short name which is inside 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) ## OPTIONS - **mode-specific-options** Each of the above modes has specific options. The complete list of options for a given mode \ can be get by running **goby 100m \** which returns a complete list of options for running the mode \ as well as a description of what this mode provides. - **-h**, **--help** Displays usage help information - **-H**, **--x-help** Displays help for dynamic options - This manual page was written by Pierre Gruet \ from the Debian ## AUTHOR project, but may be used by others.