minimap2 VS bwa-mem2

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

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences (by lh3)
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minimap2 bwa-mem2
5 2
1,707 687
- 1.6%
7.6 3.1
24 days ago about 1 month 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.

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.

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.
  • Anyone use DRAGEN-GATK?
    1 project | /r/bioinformatics | 12 Oct 2022
    If you haven’t heard of it already you may want to check out https://github.com/bwa-mem2/bwa-mem2 which is a faster version of bwa-mem. I’ve been using it for a while now and found it to be quite stable, same results as the original and the speed improvement is nice.
  • 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

What are some alternatives?

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

seqtk - Toolkit for processing sequences in FASTA/Q formats

bowtie2 - A fast and sensitive gapped read aligner

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

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

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

htslib - C library for high-throughput sequencing data formats

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

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

bwa-mem2 - The next version of bwa-mem

vg - tools for working with genome variation graphs

Klib - A standalone and lightweight C library

megahit - Ultra-fast and memory-efficient (meta-)genome assembler

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Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.
www.influxdata.com
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