Assembly Sequences with CAP3
CAP3 is a contig assembly program. It allows the assembly of long DNA reads (up to 1000 bp).
Binaries can be downloaded from http://seq.cs.iastate.edu/cap3.html
Huang, X. and Madan, A. (1999) CAP3: A DNA Sequence Assembly Program, Genome Research, 9: 868-877.
Element type: cap3
Parameters
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Output file | Write assembly results to this output file in ACE format. | result.ace | out-file | string |
| Quality cutoff for clipping | Base quality cutoff for clipping (-c). | 12 | clipping-cutoff | numeric |
| Clipping range | Set a number whose unit is base. It will get the refGenes in n bases from the peak center. (–distance). | 100 | clipping-range | numeric |
| Quality cutoff for differences | Base quality cutoff for differences (-b). | 20 | diff-cutoff | numeric |
| Maximum difference score | Max qscore sum at differences (-d). If an overlap contains numerous differences at bases of high quality, the overlap is removed. | 200 | diff-max-qscore | numeric |
| Match score factor | Affects the similarity score of an overlap (-m). | 2 | match-score-factor | numeric |
| Mismatch score factor | Affects the similarity score of an overlap (-n). | -5 | mismatch-score-factor | numeric |
| Gap penalty factor | Affects the similarity score of an overlap (-g). | 6 | gap-penalty-factor | numeric |
| Overlap similarity score cutoff | If the similarity score of an overlap is less than this cutoff (-s), the overlap is removed. | 900 | overlap-sim-score-cutoff | numeric |
| Overlap length cutoff | Overlaps must be at least this long in bp (-o). | 40 | overlap-length-cutoff | numeric |
| Overlap percent identity cutoff | Overlaps must meet or exceed this percent identity (-p). | 90 | overlap-perc-id-cutoff | numeric |
| Max number of word matches | Upper limit for the number of word matches considered (-t). Controls the trade-off between accuracy and speed. | 300 | max-num-word-matches | numeric |
| Band expansion size | CAP3 expands alignment bands by this size (-a). | 20 | band-exp-size | numeric |
| Max gap length in an overlap | Maximum length of gap in overlaps allowed (-f). | 20 | max-gap-in-overlap | numeric |
| Assembly reverse reads | Whether to consider reverse orientation reads in assembly (-r). | True | assembly-reverse | boolean |
| CAP3 tool path | Path to the CAP3 executable. | default | path | string |
| Temporary directory | Directory for temporary files. | default | tmp-dir | string |
Input/Output Ports
The element has 1 input port:
Name in GUI: Input sequences
Name in Workflow File: in-data
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Dataset name | dataset | string |
| Input URL(s) | in.url | string |