goby(1)
Sequencing data and results analysis tool
Description
GOBY
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.
MANDATORY INFORMATION
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<mem> |
Human-readable amount of memory to allocate to Goby e.g. could be 1m, 145m, 3g, ... |
<mode>
Indicates to use the mode <mode> of Goby when running. <mode> must be one of the following ones (either the long name or the short name which is inside parentheses):
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aggregate-by-peak-distance (abpd) |
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aggregate-by-peak-rpkm-difference (abprd) |
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alignment-to-annotation-counts (atac) |
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alignment-to-counts (altc) |
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alignment-to-pileup (atp) |
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alignment-to-read-set (atrs) |
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alignment-to-text (att) |
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alignment-to-transcript-counts (attc) |
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annotation-penalty (ap) |
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annotations-to-counts (antc) |
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barcode-decoder (bd) |
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base-stats (bs) |
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bisulfite-conversion (bc) |
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build-sequence-cache (bsc) |
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compact-file-stats (cfs) |
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compact-to-fasta (ctf) |
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compact-to-sam (cts) |
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compare-alignment-to-genome (catg) |
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concatenate-alignments (ca) |
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concatenate-compact-reads (ccr) |
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count-archive-to-peak-annotations (catpa) |
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count-archive-to-peak-union-annotations (catpua) |
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counts-to-bedgraph (ctb) |
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counts-to-wiggle (ctw) |
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coverage (c) |
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diff-alignments (da) |
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discover-sequence-variants |
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display-sequence-variations |
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empirical-p (ep) |
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extract-splicing-events (ese) |
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fasta-to-compact (ftc) |
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fdr (f) |
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files-to-attributes (fta) |
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heptamer-weights (hw) |
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infer-sex (hasResult) |
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last-to-compact (ltc) |
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merge-compact-alignments (mca) |
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methyl-stats (ms) |
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read-quality-stats (rqs) |
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reads-to-weights (rtw) |
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reformat-compact-reads (rcr) |
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run-parallel (rp) |
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sam-comparison (sc) |
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sam-extract-reads (ser) |
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sam-to-compact (stc) |
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sam-to-compact-old (stco) |
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sam-to-compact-samhelper (stcs) |
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sample-quality-scores (sqs) |
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sequence-variation-stats (svs) |
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sequence-variation-stats2 (svs2) |
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set-to-text (stt) |
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simulate-reads (sr) |
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sort (s) |
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sort-1 (s1) |
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split-compact-reads (scr) |
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split-fasta (sf) |
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split-transcripts (st) |
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stats |
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suggest-position-slices (sps) |
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tab-to-column-info (ttci) |
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tally-bases (tb) |
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tally-reads (tr) |
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test-r-connection (trc) |
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trim (t) |
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upgrade (u) |
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vcf-compare (vc) |
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vcf-subset (vs) |
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vcf-to-genotype-map (vtgm) |
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vcf-to-indel-set (vtis) |
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vcf-to-tab (vtt) |
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version (v) |
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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 <mode> can be get by running
goby 100m <mode>
which returns a complete list of options for running the mode <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
AUTHOR
This manual page was written by Pierre Gruet <[email protected]> from the Debian project, but may be used by others.