--alignment-stringency |
|
<[LOW, MEDIUM,HIGH]> |
A higher stringency level will tend to produce contigs with less ambiguities but will also tend to omit more sequencing reads and to generate more and shorter contigs (default: MEDIUM) |
--conflicts <[VOTE, UNKNOWN, AMBIGUTY]> |
conflicts (default: VOTE) |
-d, --destination <ClcServerObjectUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
-i, --input <ClcObjectUrl> |
Input data on server |
--include-partly <Boolean> |
Remove ends of the reference sequence(s) that do not align with any reads (default: false) |
--include-reference |
|
<[INCLUDE_REFERENCE, EXCLUDE_REFERENCE] |
|
> |
Whether to include reference sequence(s) in contig(s) or not (default: INCLUDE_REFERENCE) |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--min-length |
|
Integer: 1 <= x <= 2147483647 |
Exclude reads if less than this number of nucleotides can be aligned to the contig (default: 50) |
--reference <ClcObjectUrl> |
Reference sequences or genome track |
--residues <Integer> |
The number of overhanging residues to keep from the reference sequence(s) (default: 100) |
--use-trim <Boolean> |
Exclude regions of sequencing reads which have previously been trimmed (default: false) |
