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
- This manual page was written by Pierre Gruet <[email protected]> from the Debian
AUTHOR
project, but may be used by others.