| Name | countess-minimap2 JSON |
| Version |
0.0.14
JSON |
| download |
| home_page | None |
| Summary | Sequence Alignment Plugin for CountESS, based in Minimap2 |
| upload_time | 2024-08-27 22:51:03 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.10 |
| license | BSD-3-Clause |
| keywords |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
|
# CountESS MiniMap2 Plugin v0.0.14
This is a plugin to allow [MiniMap2](https://github.com/lh3/minimap2)
to be used from within [CountESS](https://github.com/CountESS-Project/CountESS/)
This might be useful, but it also stands as a handy example of how to write
a CountESS plugin which wraps an external Python library.
## Parameters
### Output Column Prefix
The default output column prefix is `mm` but this can be changed.
### Ref FA / Ref MMI
A local FASTA or MMI file to look up the sequences in.
Acceptable formats are MMI or FASTA, optionally gzipped.
### Req Sequence
Alternatively, enter a single reference DNA sequence directly here.
### Preset
See [minimap2 Preset Options](https://lh3.github.io/minimap2/minimap2.html#8)
### Minimum Match Length
Reject matches with an overall length (`mm_r_en - mm_r_st`) less than this.
### Drop Unmatched
Rows with no matches will be dropped.
## Output Columns
### `mm_ctg`
The matched location.
### `mm_r_st`, `mm_r_en`
Start and end positions of the matched sequence.
### `mm_strand`
`1` if query/target on the same strand.
`-1` if opposite.
`0` if unknown.
### `mm_cigar`
CIGAR string expressing the differences within the match. Note that not all differences are
encoded in the CIGAR string, for a more detailed description of what variations are present see
the next two fields.
### `mm_cs`
A difference string as documented in the [Minimap2 Output Format](https://lh3.github.io/minimap2/minimap2.html#10) section.
### `mm_hgvs`
The difference string translated into HGVS format relative to the matched location.
## License
BSD 3-clause. See [LICENSE.txt](LICENSE.txt)
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