CountESS MiniMap2 Plugin v0.0.14
This is a plugin to allow MiniMap2 to be used from within 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
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 section.
mm_hgvs
The difference string translated into HGVS format relative to the matched location.
License
BSD 3-clause. See LICENSE.txt
1 maintainer
Metadata
1 maintainer
Release files for countess-minimap2 0.1.1
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Release files / countess_minimap2-0.1.1.tar.gz
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