minimap2
bwa-mem2
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| minimap2 | bwa-mem2 | |
|---|---|---|
| 5 | 2 | |
| 1,684 | 676 | |
| - | 1.5% | |
| 7.8 | 2.6 | |
| 6 days ago | 4 months ago | |
| C | C++ | |
| GNU General Public License v3.0 or later | GNU General Public License v3.0 or later |
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
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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
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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?
seqtk - Toolkit for processing sequences in FASTA/Q formats
bowtie2 - A fast and sensitive gapped read aligner
seqstats - Quick summary statistics on fasta/fastq(.gz) files
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
slivar - genetic variant expressions, annotation, and filtering for great good.
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.
htslib - C library for high-throughput sequencing data formats
bwa-mem2 - The next version of bwa-mem
vg - tools for working with genome variation graphs
Klib - A standalone and lightweight C library
megahit - Ultra-fast and memory-efficient (meta-)genome assembler