--auto-detect-paired-distances <Boolean> |
Determine appropriate paired distances as part of the assembly process. This is done individually for each data set. If this option is not selected, the assembler will use the paired distance information specified on the input data. (default: true) |
--bubblesize |
|
Integer: 1 <= x <= 5000 |
Bubble size used in the de Bruijn-Graph. Increase this when expecting many SNP's or systematic errors. (default: 50) |
--bubblesize-auto <Boolean> |
Bubble size will be calculated. (default: true) |
--create-report-1 <Boolean> |
Create a summary report showing contig statistics. (default: true) |
--create-report-2 <Boolean> |
Create a summary report showing number of mapped reads etc. (default: true) |
--create-report-3 <Boolean> |
Create a summary report showing contig statistics and number of mapped reads to the contigs etc. (default: true) |
--create-sequence-list <Boolean> |
Create sequencelist containing reads that do not match the reference. (default: false) |
-d, --destination <ClcServerObjectUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
--guidance-only <ClcObjectUrl> |
Select reads only used as guidance if they contain many errors. |
-i, --input <ClcObjectUrl> |
Input data on server |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--long-reads-alignment-mode <[LOCAL, GLOBAL]> |
Alignment mode can be "local" or "global".For global end gaps are treated as mismatches and for local end gaps will not have additional cost. (default: LOCAL) |
--long-reads-deletion-cost |
|
Integer: 1 <= x <= 3 |
Cost of creating a deletion (1, 2, or 3). (default: 3) |
--long-reads-insertion-cost |
|
Integer: 1 <= x <= 3 |
Cost of creating an insertion (1, 2, or 3). (default: 3) |
--long-reads-length-fraction |
|
Double: 0.0 < x <= 1.0 |
Minimum length fraction of a read that must match the reference sequence. (default: 0.5) |
--long-reads-match-cost |
|
Integer: 1 <= x <= 3 |
Cost of creating a mismatch (1, 2, or 3). (default: 2) |
--long-reads-similarity-fraction |
|
Double: 0.0 < x <= 1.0 |
Minimum fraction of similarity between read and reference sequence. (default: 0.8) |
--map-reads-to-contigs <[SIMPLE, MAP_BACK]> |
Mapping can be "SIMPLE" or "MAP_BACK". Only simple contig sequences or map reads to the contig sequences from the de novo assembly. (default: MAP_BACK) |
--match-mode <[IGNORE, RANDOM]> |
Whether a read with more than one match is assigned randomly to a match region or discarded. Possible values: random and ignore. (default: RANDOM) |
--minimum-contig-length |
|
Integer: >= 1 |
Mininum size of assembled contig. (default: 200) |
--perform-scaffolding <Boolean> |
Perform scaffolding based on paired reads. If the input data does not contain paired data, scaffolding cannot be selected. (default: true) |
--update-contigs <Boolean> |
The contigs will be adjusted by the mapped reads. (default: true) |
--wordsize |
|
Integer: 12 <= x <= 64 |
Word size used to construct the de Bruijn-Graph. (default: 20) |
--wordsize-auto <Boolean> |
Word size will be calculated. (default: true) |
