Minimap2

Introduction

Minimap2 (Li 2018) is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.

Available on Crunchomics: Minimap2 version 2.24-r1122 installed

Installation

If you want to install minimap2 on your own, its best to install it via mamba:

#setup new conda environment, which we name kraken2
mamba create --name minimap2 -c bioconda minimap2

Usage

For detailed usage information, check out the minimap2 manual.

Input:

  • Minimap takes both fastq as well as fasta sequences as input
#example of mapping input sequences against sequences of the SILVA 16S database
minimap2 -cx map-ont -t <nr_of_threads> \
        -N 10 -K 25M \
        silva-ref.fasta \
        my_seqs.fastq \
        -o output.paf

Used options:

  • -x map-ont: Run minimap optimized for Nanopore reads
  • -c: output is generated in PAF format, use -aif you prefer the output in SAM format
  • -N: lso retain up to -N [=10] top secondary mappings
  • -K: Read -K [=25M] query bases
  • …

There are many different ways to run minimap2, so check out the minimap2 manual for all options.

References

Li, Heng. 2018. “Minimap2: Pairwise Alignment for Nucleotide Sequences.” Bioinformatics 34 (18): 3094–3100. https://doi.org/10.1093/bioinformatics/bty191.