fastq-dump [options] <accession>
| General: | ||||
| -h | | | --help | Displays ALL options, general usage, and version information. | |
| -V | | | --version | Display the version of the program. | |
| Data formatting: | ||||
| --split-files | Dump each read into separate file. Files will receive suffix corresponding to read number. | |||
| --split-spot | Split spots into individual reads. | |||
| --fasta <[line width]> | FASTA only, no qualities. Optional line wrap width (set to zero for no wrapping). | |||
| -I | | | --readids | Append read id after spot id as 'accession.spot.readid' on defline. | |
| -F | | | --origfmt | Defline contains only original sequence name. | |
| -C | | | --dumpcs <[cskey]> | Formats sequence using color space (default for SOLiD). "cskey" may be specified for translation. | |
| -B | | | --dumpbase | Formats sequence using base space (default for other than SOLiD). | |
| -Q | | | --offset |
Offset to use for ASCII quality scores. Default is 33 ("!"). | |
| Filtering: | ||||
| -N | | | --minSpotId |
Minimum spot id to be dumped. Use with "X" to dump a range. | |
| -X | | | --maxSpotId |
Maximum spot id to be dumped. Use with "N" to dump a range. | |
| -M | | | --minReadLen |
Filter by sequence length >= |
|
| --skip-technical | Dump only biological reads. | |||
| --aligned | Dump only aligned sequences. Aligned datasets only; see sra-stat. | |||
| --unaligned | Dump only unaligned sequences. Will dump all for unaligned datasets. | |||
| Workflow and piping: | ||||
| -O | | | --outdir |
Output directory, default is current working directory ('.'). | |
| -Z | | | --stdout | Output to stdout, all split data become joined into single stream. | |
| --gzip | Compress output using gzip. | |||
| --bzip2 | Compress output using bzip2. | |||