minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences (by 7PintsOfCherryGarcia)
bwa-mem2
The next version of bwa-mem (by bwa-mem2)
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| minimap2 | bwa-mem2 | |
|---|---|---|
| 1 | 2 | |
| 0 | 676 | |
| - | 1.8% | |
| 1.8 | 2.6 | |
| over 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.
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 2021-11-21.
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sqzlib - kseq compatible DNA fastA/Q encoding and compression library
Most importantly, sqzlib is fully compatible with klib/kseq.h one of the highest performance fastA/Q parsers. This means that any application that uses kseq.h for fastA/Q parsing, can be easily modified to use sqzlib instead. You can find patched versions of seqstats, minimap2, and bwa-mem2 in my github, or you can patch them yourself with the included patches.
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.
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Anyone use DRAGEN-GATK?
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.
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Software Development Project
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:
bwa-mem2 - The next version of bwa-mem
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
seqstats - Quick summary statistics on fasta/fastq(.gz) files
bowtie2 - A fast and sensitive gapped read aligner
sqzlib - Blocked bases fastX encoding and compression
htslib - C library for high-throughput sequencing data formats
Klib - A standalone and lightweight C library
edlib - Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
vg - tools for working with genome variation graphs
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
GenomicSQLite - Genomics Extension for SQLite