abi-dump [options] <accession>
General: | ||||
-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). | |
Filtering: | ||||
--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. |