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)
Bioinformatics read-aligners Genomics C++
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bwa-mem2

The next version of bwa-mem (by bwa-mem2)
Bioinformatics Genomics sequence-alignment
Source Code
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bowtie2 bwa-mem2
2 2
618 676
- 1.8%
7.6 2.6
5 days ago 4 months 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 2023-09-14.

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 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

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

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

seq - A high-performance, Pythonic language for bioinformatics

htslib - C library for high-throughput sequencing data formats

fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

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

IntaRNA - Efficient target prediction incorporating accessibility of interaction sites

vg - tools for working with genome variation graphs

kraken2 - The second version of the Kraken taxonomic sequence classification system

bowtie2 vs STAR bwa-mem2 vs minimap2 bowtie2 vs megahit bwa-mem2 vs minimap2 bowtie2 vs seq bwa-mem2 vs htslib bowtie2 vs fastp bwa-mem2 vs edlib bowtie2 vs IntaRNA bwa-mem2 vs vg bowtie2 vs kraken2 bwa-mem2 vs megahit