SRA Toolkit DocumentationBack to List of the Tools
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.|
|-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.|
Prints the first 5 spots ("-X 5") to standard out ("-Z") with the original formatting for reads ("-F").
abi-dump -Z -X 5 -F SRR390728
Possible errors and their solution:
This error indicates that the .sra file cannot be found. Confirm that the path to the file is correct.
item not found while constructing within virtual database module - the path 'SRR*' cannot be opened as database or table
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.
failed with curl-error 'CURLE_COULDNT_RESOLVE_HOST'