--3-prime-bases |
|
Integer: >= 1 |
Number of nucleotides to remove. (default: 1) |
--3-prime-trim <Boolean> |
Remove fixed number of nucleotides from the 3' terminus (default: false) |
--5-prime-bases |
|
Integer: >= 1 |
Number of nucleotides to remove. (default: 1) |
--5-prime-trim <Boolean> |
Remove fixed number of nucleotides from the 5' terminus (default: false) |
--ambiguous-limit |
|
Integer: >= 0 |
Maximum number of ambiguous nucleotides allowed after trimming. Decreasing this value causes more stringent trimming (default: 2) |
--ambiguous-trim <Boolean> |
Trim ends based on the presence of ambiguity characters, e.g. N (default: true) |
--create-report <Boolean> |
Create a report (default: true) |
-d, --destination <ClcServerObjectUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
--discard-long <Boolean> |
Discard long reads (default: false) |
--discard-long-limit |
|
Integer: >= 1 |
Discard all reads which consist of more residues than the given threshold (default: 1000) |
--discard-short <Boolean> |
Discard short reads (default: false) |
--discard-short-limit |
|
Integer: >= 0 |
Discard all reads which consist of less residues than the given threshold (default: 15) |
-i, --input <ClcObjectUrl> |
Input data on server |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--quality-limit |
|
Double: 0.0 <= x <= 1.0 |
Decreasing this value causes more stringent trimming (default: 0.05) |
--quality-trim <Boolean> |
Trim ends using the prediction reliability calculated by the base-caller (default: true) |
--readthrough-trimming <Boolean> |
Detects overlaps in paired reads and trims the non-overlapping part away. (default: true) |
--save-broken-pairs <Boolean> |
Create a sequence list containing reads from paired reads where one read is completely trimmed (default: false) |
--save-discarded <Boolean> |
Create a sequence list containing the completely trimmed sequences (default: false) |
--trim-adapter-list <ClcObjectUrl> |
List of adapters to be used for trimming. Can be created in the Workbench in File -> New -> Adapter List |
