minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences (by lh3)
miniprot
Align proteins to genomes with splicing and frameshift (by lh3)
| minimap2 | miniprot | |
|---|---|---|
| 5 | 1 | |
| 1,688 | 299 | |
| - | - | |
| 7.6 | 5.8 | |
| 10 days ago | 22 days ago | |
| C | C | |
| GNU General Public License v3.0 or later | MIT License |
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.
miniprot
Posts with mentions or reviews of miniprot.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-02-06.
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Identifying potential genes involved in nociception
Alternatively, there is a new tool out from Heng Li (bioinformatics godfather) which apparently does good quality mapping of proteins to references (miniprot). You could download your 'painless' genes from Drosophila and use this tool to look for them in your reference (similar to above, except this tool is apparently better able to handle larger differences).
What are some alternatives?
When comparing minimap2 and miniprot you can also consider the following projects:
bwa-mem2 - The next version of bwa-mem
seqtk - Toolkit for processing sequences in FASTA/Q formats
Liftoff - An accurate GFF3/GTF lift over pipeline
seqstats - Quick summary statistics on fasta/fastq(.gz) files
slivar - genetic variant expressions, annotation, and filtering for great good.
MethylDackel - A (mostly) universal methylation extractor for BS-seq experiments.
bwa-mem2 - The next version of bwa-mem
Klib - A standalone and lightweight C library
Bitgrid - Bitgrid - a new model of computation
biowasm - WebAssembly modules for genomics
surge - Synthesizer plug-in (previously released as Vember Audio Surge)