bwa-mem2 VS vg

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

bwa-mem2

The next version of bwa-mem (by bwa-mem2)
Bioinformatics Genomics sequence-alignment
Source Code
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vg

tools for working with genome variation graphs (by vgteam)
variation-graph Graph genome-graph Genomics Dna
Source Code
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bwa-mem2 vg
2 2
676 1,060
1.8% 1.7%
2.6 9.4
4 months ago 4 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.
  • 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

vg

Posts with mentions or reviews of vg. We have used some of these posts to build our list of alternatives and similar projects.
  • VG v1.36.0 just released!
    1 project | /r/UCSC | 11 Nov 2021
    Just released! VG v1.36.0, available at https://github.com/vgteam/vg/releases/tag/v1.36.0 offers improvements vg clip, including an option for clipping out big deletion edges while skipping multiple specified alleles.
  • VG v1.34.0 Release!
    1 project | /r/UCSC | 18 Aug 2021
    Just out! vg v1.34.0 code-named "Arguello" is available now: https://github.com/vgteam/vg/releases/tag/v1.34.0

What are some alternatives?

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

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

QuickQanava - :link: C++17 network / graph visualization library - Qt6 / QML node editor.

bowtie2 - A fast and sensitive gapped read aligner

euler - A distributed graph deep learning framework.

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

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

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

GenomicSQLite - Genomics Extension for SQLite

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

bwa-mem2 vs minimap2 vg vs QuickQanava bwa-mem2 vs bowtie2 vg vs euler bwa-mem2 vs minimap2 vg vs seq bwa-mem2 vs htslib vg vs bowtie2 bwa-mem2 vs edlib bwa-mem2 vs megahit bwa-mem2 vs GenomicSQLite bwa-mem2 vs seqstats