minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences (by lh3)
slivar
genetic variant expressions, annotation, and filtering for great good. (by brentp)
| minimap2 | slivar | |
|---|---|---|
| 5 | 1 | |
| 1,998 | 262 | |
| 1.5% | -0.4% | |
| 8.6 | 2.9 | |
| about 1 month ago | 10 days ago | |
| C | Nim | |
| 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.
slivar
Posts with mentions or reviews of slivar.
We have used some of these posts to build our list of alternatives
and similar projects.
-
Help on installation of GEMINi
Looks like they’ve broken the install at some point. If you check the GitHub for Gemini it recommends you replace it with slivar https://github.com/brentp/slivar
What are some alternatives?
When comparing minimap2 and slivar you can also consider the following projects:
bwa-mem2 - The next version of bwa-mem
bwa - Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Bitgrid - Bitgrid - a new model of computation
open-cravat - A modular annotation tool for genomic variants
stock-exchange - Personal stock exchange on your laptop!
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.