README.md

Minimap2_index_modifier

Minimap2_index_modifier is a fork of alignment tool minimap2. Unlike the original tool, this can use the variants defined in the VCF file when generating the index, for more accurate alignment.

Minimap2_index_modifier can be used in the same way as the original minimap2.
To create a modified index use additional parameter --vcf-file-with-variants <vcf-file>.

minimap2 -d index.mmi --vcf-file-with-variants input.vcf.gz reference.fasta

Use flag --parse-haplotype if your VCF contains phased haplotypes.

Contents

• Installation
  • Compiling from source
  • Docker
  • Dockerhub
• Pre-built indexes
• Tests
• Publication

Installation

Compiling from source

To compile from source, use this version of tools:

• GCC/G++ 11.4.0+
• HTSlib v1.17

Command to compile:

cd minimap2_index_modifier && make

Docker

Clone this repository and build a Docker image as follows.

docker build -t minimap2_index_modifier:2.24 .

Dockerhub

Clone Docker image from Dockerhub.

docker pull egorguga/minimap2_index_modifier:2.24

Pre-built indexes

This link contains pre-built modified indexes for next references:

• GRCh38 (GCA_000001405.15)
• GRCh37 (hs37d5)

Tests

See test/tests.md for more details.

Publication

Guguchkin, E., Kasianov, A., Belenikin, M. et al. Enhancing SNV identification in whole-genome sequencing data through the incorporation of known genetic variants into the minimap2 index. BMC Bioinformatics 25, 238 (2024). https://doi.org/10.1186/s12859-024-05862-y