goby - Sequencing data and results analysis tool
goby <mem> <mode> [OPTIONS]
Goby provides facilities to manage sequencing data and ease
the implementation of data analysis pipelines.
- <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)
- 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
This manual page was written by Pierre Gruet
<pgt@debian.org> from the Debian project, but may be used by
others.