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.

                                            08-08-2021                                    GOBY(1)