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Illumina Complete Long Read presets (#1069)

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* Implements a transition-aware alignment scoring scheme and configuration presets for ICLR

* Fix to enable use of general scoring matrix in ksw as suggested by lh3

---------

Co-authored-by: koadman <>
This commit is contained in:
Aaron Darling
2023-06-04 11:06:15 -04:00
committed by GitHub
co-authored by koadman
parent e28a55be86
commit ace990c381
5 changed files with 32 additions and 6 deletions
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README.md
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@@ -139,12 +139,15 @@ parameters at the same time. The default setting is the same as `map-ont`.
```sh
minimap2 -ax map-pb ref.fa pacbio-reads.fq > aln.sam # for PacBio CLR reads
minimap2 -ax map-ont ref.fa ont-reads.fq > aln.sam # for Oxford Nanopore reads
minimap2 -ax map-iclr ref.fa iclr-reads.fq > aln.sam # for Illumina Complete Long Reads
```
The difference between `map-pb` and `map-ont` is that `map-pb` uses
homopolymer-compressed (HPC) minimizers as seeds, while `map-ont` uses ordinary
minimizers as seeds. Emperical evaluation suggests HPC minimizers improve
minimizers as seeds. Empirical evaluation suggests HPC minimizers improve
performance and sensitivity when aligning PacBio CLR reads, but hurt when aligning
Nanopore reads.
Nanopore reads. `map-iclr` uses an adjusted alignment scoring matrix that
accounts for the low overall error rate in the reads, with transversion errors
being less frequent than transitions.
#### <a name="map-long-splice"></a>Map long mRNA/cDNA reads