countess-minimap2 0.0.13

Sequence Alignment Plugin for CountESS, based in Minimap2

CountESS MiniMap2 Plugin v0.0.10

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

See minimap2 Preset Options

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