minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences (by lh3)
bwa-mem2
The next version of bwa-mem (by 7PintsOfCherryGarcia)
| minimap2 | bwa-mem2 | |
|---|---|---|
| 5 | 1 | |
| 1,688 | 0 | |
| - | - | |
| 7.6 | 3.2 | |
| 7 days ago | over 2 years 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 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.
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 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.
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
seqtk - Toolkit for processing sequences in FASTA/Q formats
Klib - A standalone and lightweight C library
seqstats - Quick summary statistics on fasta/fastq(.gz) files
sqzlib - Blocked bases fastX encoding and compression
slivar - genetic variant expressions, annotation, and filtering for great good.
MethylDackel - A (mostly) universal methylation extractor for BS-seq experiments.
Bitgrid - Bitgrid - a new model of computation
biowasm - WebAssembly modules for genomics