GOBY(1)

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

<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):

•   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 <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 <pgt@debian.org> from the Debian
    project, but may be used by others.