bowtie VS bwa-mem2

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

bowtie

An ultrafast memory-efficient short 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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bowtie bwa-mem2
1 2
252 673
- 1.3%
10.0 2.6
almost 2 years ago 4 months 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.

bowtie

Posts with mentions or reviews of bowtie. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2022-09-24.

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

What are some alternatives?

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

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

bowtie2 - A fast and sensitive gapped read aligner

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

htslib - C library for high-throughput sequencing data formats

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

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

vg - tools for working with genome variation graphs

GenomicSQLite - Genomics Extension for SQLite

IntaRNA - Efficient target prediction incorporating accessibility of interaction sites

bwa - Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

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

nanopolish - Signal-level algorithms for MinION data

bwa-mem2 vs minimap2 bwa-mem2 vs bowtie2 bwa-mem2 vs minimap2 bwa-mem2 vs htslib bwa-mem2 vs edlib bwa-mem2 vs seqstats bwa-mem2 vs vg bwa-mem2 vs GenomicSQLite bwa-mem2 vs IntaRNA bowtie vs bwa bwa-mem2 vs megahit bowtie vs nanopolish