--annotate-conflicts <Boolean> |
Add conflict annotations to the assembly. (default: false) |
--bubblesize |
|
Integer: 50 <= 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) |
--conflict-resolution-mode <String> |
Conflict resolution possible values: Unknown nucleotide, Ambiguity nucleotides and Vote. (default: Vote) |
--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 <ClcUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
--guidance-only <ClcUrl> |
Select paired reads only used as guidance if they contain many errors. |
-i, --input <ClcUrl> |
Input data on server |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--long-reads-alignment-mode |
|
<[LOCAL,GLOBAL, SEMIGLOBAL]> |
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-color-error-cost |
|
Integer: 1 <= x <= 3 |
Cost of creating color error (1, 2, or 3). (default: 3) |
--long-reads-color-space <Boolean> |
Perform color space alignment for relevant data sets. (default: true) |
--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-as-long-reads <Boolean> |
Internally used for gapped alignments. (default: false) |
--map-as-single-reads <Boolean> |
Internally used as gapped alignments. (default: false) |
--map-reads-to-contigs |
|
<[SIMPLE,MAP_BACK]> |
Mapping can be "simple" or "map". Only simple contig sequences or map reads to the contig sequences from the de novo assembly. (default: MAP_BACK) |
--match-mode |
|
<[IGNORE, RANDOM,UNPAIREDCLOSEST]> |
Whether a read with more than one match is assigned randomly to a match region or discarded. Possible values: random and ignore. (default: RANDOM) |
--maximum-alignment-count |
|
Integer: >= 1 |
Max reported alignments (internal use only). (default: 1) |
--minimum-contig-length |
|
Integer: >= 1 |
Mininum size of assembled contig. (default: 200) |
--perform-scaffolding <Boolean> |
Perform scaffolding based on paired reads. (default: true) |
--score-limit-offset |
|
Integer: >= 0 |
Lowers the max limit of the very short reads. By default the limit is 0 for reads smaller than 22 nt, 1 for 22-25 nt and 2 for 26-29 nt. you can lower this limit by x nt. (default: 0) |
--strand-specific <Boolean> |
Strand specific (default: false) |
--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) |