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
|
<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.