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SLiMSuite Documentation
Please note that command documentation sometimes lags behind the latest module versions. Click on module names to check current documentation.
cmd: batch
Option Type: [?]{docs:?} FILELIST GLIST LIST
Modules: orcfinder rje_misc rje_paml rje_price rje_teaching qslimfinder_V1.9 slimfinder_V4.9 slimprob_V1.4 rje_iridis rje_samtools rje_slimcore snp_mapper fiesta qslimfinder slimfarmer slimfinder slimmutant slimprob slimsearch smrtscape_V1 smrtscape
| Module | Option | Description | Default |
|---|---|---|---|
| fiesta | batch=LIST |
List of EST libraries to search (will use seqin if none given) | |
| orcfinder | batch=LIST |
List of files to search, wildcards allowed. (Over-ruled by seqin=FILE.) | *.dat,*.fas |
| qslimfinder | batch=LIST |
List of files to search, wildcards allowed. (Over-ruled by seqin=FILE.) | *.dat,*.fas |
| qslimfinder_V1.9 | batch=LIST |
List of files to search, wildcards allowed. (Over-ruled by seqin=FILE.) | *.dat,*.fas |
| rje_iridis | [batch=?]{docs:?} |
? |
|
| rje_misc | batch=GLIST |
List of files to process for relevant task | |
| rje_paml | batch=LIST |
List of files to batch run on | '*.fas' |
| rje_price | batch=LIST |
List of alignment files to use as input | *.fas,*.fasta |
| rje_samtools | batch=FILELIST |
List of MPileup/SAM files to be parsed and filtered (e.g. *.pileup) | |
| rje_slimcore | batch=LIST |
List of files to search, wildcards allowed. | *.dat,*.fas |
| rje_teaching | [batch=?]{docs:?} |
? |
|
| slimfarmer | [batch=?]{docs:?} |
? |
|
| slimfinder | batch=FILELIST |
List of files to search, wildcards allowed. (Over-ruled by seqin=FILE.) | *.dat,*.fas |
| slimfinder_V4.9 | batch=LIST |
List of files to search, wildcards allowed. (Over-ruled by seqin=FILE.) | *.dat,*.fas |
| slimmutant | batch=FILELIST |
List of mutfiles to run in batch mode. Wildcards allowed. | |
| slimprob | batch=FILELIST |
List of files to search, wildcards allowed. (Over-ruled by seqin=FILE.) | *.dat,*.fas |
| slimprob_V1.4 | batch=LIST |
List of sequence files for batch input (wildcard * permitted) | |
| slimsearch | batch=LIST |
List of sequence files for batch input (wildcard * permitted) | |
| smrtscape | batch=FILELIST |
Batch input of multiple subread fasta files (wildcards allowed) if seqin=None | basefile.fofn |
| smrtscape_V1 | batch=FILELIST |
Batch input of multiple subread fasta files (wildcards allowed) if seqin=None | |
| snp_mapper | batch=LIST |
List of alignment files to read X.aln - must have X_polymorphisms.txt too | *.aln |
© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.