skip to main content

SRA Toolkit Documentation

Back to List of the Tools

Tool: abi-dump

abi-dump [options] <path/file> [<path/file> ...]
abi-dump [options] <accession>
Frequently Used Options:
-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 <rowid> Minimum spot id.
-X | --maxSpotId <rowid> 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 <path> 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.
Use examples:
abi-dump -Z -X 5 -F SRR390728
Prints the first 5 spots ("-X 5") to standard out ("-Z") with the original formatting for reads ("-F").
Possible errors and their solution:
item not found while constructing within virtual database module - the path 'SRR*' cannot be opened as database or table
This error indicates that the .sra file cannot be found. Confirm that the path to the file is correct.
failed with curl-error 'CURLE_COULDNT_RESOLVE_HOST'
The toolkit is attempting to contact or download data from NCBI, but is unable to connect. Please confirm that your computer or server has Internet connectivity.