Reference genome database for Minimap2
======

Minimap2 is a rapid aligner for short and long DNA and mRNA sequences against a
large database.

 - Website: https://github.com/lh3/minimap2
 - Citation: Li H. Minimap2: pairwise alignment for nucleotide sequences.
   Bioinformatics. 2018. 34(18): 3094-100.

Built using Minimap2 v2.24.

Two variants of database (index) are provided:

1. `WoLr2.mmi`: Default index:

```
minimap2 input.fna -d WoLr2.mmi --seed 42
```

2. `WoLr2.sr.mmi`: Index optimized for short read (sr) alignment:

```
minimap2 input.fna -d WoLr2.sr.mmi --seed 42 -ax sr
```

Typical alignment command:

```
minimap2 -t # -x sr WoLr2.sr input.R1.fq.gz input.R2.fq.gz -a -o output.sam \
  --seed 42
```