mmistat v0.1.0
mmistat
minimap2 index file (.mmi) statistics
Installation
Download the latest release from GitHub Releases.
Note: Binaries for MacOS are not statically linked. To use on macOS, please build from source.
Usage
Create a minimap2 index file with the -d
option:
# For Oxford Nanopore reads
minimap2 -x map-ont -d MT-human-ont.mmi test/MT-human.fa
# For PacBio reads
minimap2 -x map-pb -d MT-human-pb.mmi test/MT-human.fa
Then run mmistat
on the map-ont index file:
mmistat MT-human-ont.mmi
Magic number (raw): "MMI\u0002"
MMI Header:
k-mer size: 15
Seed width: 10
Bucket bits: 14
Number of sequences: 1
Flags: 0x0
Sequences:
Idx Name Length
[1] MT_human 16569
Run mmistat
on the map-pb index file:
mmistat MT-human-pb.mmi
Magic number (raw): "MMI\u0002"
MMI Header:
k-mer size: 19
Seed width: 10
Bucket bits: 14
Number of sequences: 1
Flags: 0x1
Sequences:
Idx Name Length
[1] MT_human 16569
You can see that the k-mer size differs between the two index files.
The output also shows the names and lengths of the chromosomes.
This allows you to verify that the index file is as expected.
Build
Crystal version
The Crystal version is faster because it only parses the header.
It is expected to output the same results as the C version.
crystal build mmistat.cr
C version (for testing)
The C version is reliable because it uses minimap2 as a library.
make
License
MIT
The project includes code generated by AI.
mmistat
- 0
- 0
- 0
- 0
- 0
- 25 days ago
- January 9, 2025
MIT License
Thu, 03 Jul 2025 11:04:29 GMT