bowtie2 VS bwa-mem2

Compare bowtie2 vs bwa-mem2 and see what are their differences.

bowtie2

A fast and sensitive gapped read aligner (by BenLangmead)

bwa-mem2

The next version of bwa-mem (by bwa-mem2)
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bowtie2 bwa-mem2
1 2
500 588
- 1.2%
8.3 0.0
14 days ago 22 days ago
C++ C++
GNU General Public License v3.0 only 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.

bowtie2

Posts with mentions or reviews of bowtie2. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2021-04-25.

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 | reddit.com/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 bowtie2 and bwa-mem2 you can also consider the following projects:

STAR - RNA-seq aligner

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

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

seq - A high-performance, Pythonic language for bioinformatics

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

GenomicSQLite - Genomics Extension for SQLite

Klib - A standalone and lightweight C library

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