bwa-mem2 VS minimap2

Compare bwa-mem2 vs minimap2 and see what are their differences.

bwa-mem2

The next version of bwa-mem (by bwa-mem2)

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences (by lh3)
Our great sponsors
bwa-mem2 minimap2
2 5
660 1,620
1.7% -
2.6 6.0
2 months ago 29 days ago
C++ C
GNU General Public License v3.0 or later GNU General Public License v3.0 or later
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.

bwa-mem2

Posts with mentions or reviews of bwa-mem2. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2022-06-28.
  • Software Development Project
    2 projects | /r/bioinformatics | 28 Jun 2022
    I’ve recently switched to bwa mem2 and the speed increase is nice for what is basically a drop in replacement (after a bit of validation to make sure that was true). https://github.com/bwa-mem2/bwa-mem2

minimap2

Posts with mentions or reviews of minimap2. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2023-11-06.

What are some alternatives?

When comparing bwa-mem2 and minimap2 you can also consider the following projects:

bowtie2 - A fast and sensitive gapped read aligner

minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences

seqstats - Quick summary statistics on fasta/fastq(.gz) files

slivar - genetic variant expressions, annotation, and filtering for great good.

seqtk - Toolkit for processing sequences in FASTA/Q formats

MethylDackel - A (mostly) universal methylation extractor for BS-seq experiments.

htslib - C library for high-throughput sequencing data formats

bwa-mem2 - The next version of bwa-mem

edlib - Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

Klib - A standalone and lightweight C library

vg - tools for working with genome variation graphs