denovo_assembly

--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)