Fetch Data


abi-dump [options] <path/file> [<path/file> ...]


-h | --help Displays ALL options, general usage, and version information.
-V | --version Display the version of the program.
Data formatting:
-F | --origfmt Excludes SRR accession on defline (read id).
--spot-groups <[list]> Filter by spot group (read group): name[,...].
-N | --minSpotId Minimum spot id.
-X | --maxSpotId Maximum spot id.
-R | --read-filter <[filter]> Split into files by filter value: pass|reject|criteria|redacted.
-B | --noDotReads Do not output reads consisting mostly of dots.
-W | --noclip Do not clip quality left and right for spot.
Workflow and piping:
-G | --spot-group Split into files by spot group (read group).
-K | --keep-empty-files Do not delete empty files.
-O | --outdir Output directory, default is working directory ('.').
-T | --group-in-dirs Split into subdirectories instead of files.
-Z | --stdout Output to stdout, all split data become joined into single stream.
--gzip Compress output using gzip.
--bzip2 Compress output using bzip2.

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