bwa-mem2
The next version of bwa-mem (by bwa-mem2)
minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences (by lh3)
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| bwa-mem2 | minimap2 | |
|---|---|---|
| 2 | 5 | |
| 674 | 1,679 | |
| 1.5% | - | |
| 2.6 | 7.8 | |
| 4 months ago | 13 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.
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.
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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
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 2023-11-06.
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Ask HN: Comment here about whatever you're passionate about at the moment
Interested as well! But the future is not so dark, things like e.g. https://github.com/lh3/minimap2 are a breath of fresh air.
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BLAST 10,000 genes?
No experience with this maybe try minimap2(https://github.com/lh3/minimap2) if this doesn't work fall back on blast/blat
- Truncating genome fastas to just overlapping regions
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Alignment of long reads to plasmid and generation of consensus sequence.
You can try minimap2 to align your long reads to your expected plasmid
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Questions about WGS mapping
It sounds like the mapping wasn't very good, you might want to try minimap2 as it is a newer algorithm.
What are some alternatives?
When comparing bwa-mem2 and minimap2 you can also consider the following projects:
bowtie2 - A fast and sensitive gapped read aligner
slivar - genetic variant expressions, annotation, and filtering for great good.
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
seqstats - Quick summary statistics on fasta/fastq(.gz) files
htslib - C library for high-throughput sequencing data formats
seqtk - Toolkit for processing sequences in FASTA/Q formats
edlib - Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
MethylDackel - A (mostly) universal methylation extractor for BS-seq experiments.
bwa-mem2 - The next version of bwa-mem
vg - tools for working with genome variation graphs
Klib - A standalone and lightweight C library