libdna
minimap2
| libdna | minimap2 | |
|---|---|---|
| 2 | 5 | |
| 20 | 1,691 | |
| - | - | |
| 7.4 | 7.6 | |
| 3 months ago | 7 days ago | |
| C | C | |
| MIT License | GNU General Public License v3.0 or later |
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libdna
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A good, fast hash for nucleotides triplet converted to 0, 1, 3, 2 using `3 & (nuc << 1)`
While that works for the canonical bases your method won't support CCN which should give Proline. Hence, for my implementation I have opted for a slower but more general approach. As protein coding sequences are usually short performance isn't an issue, really.
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Counting the number of matching characters in two ASCII strings
In Bioinformatics, if you now the number of mismatching characters between two strings of DNA your can compute their evolutionary distance. As DNA is long, easily a few megabytes, computing such a hamming distance via SIMD really pays of. Here is my implementation if anyone is interested: https://github.com/kloetzl/libdna
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.
What are some alternatives?
samtools - [Moved to: https://github.com/ingolia/SamTools]
bwa-mem2 - The next version of bwa-mem
htslib - C library for high-throughput sequencing data formats
seqtk - Toolkit for processing sequences in FASTA/Q formats
samtools - Tools (written in C using htslib) for manipulating next-generation sequencing data
seqstats - Quick summary statistics on fasta/fastq(.gz) files
pn2codon - Python Rust FFI for reverse-translating Amino Acid sequences to DNA sequences
slivar - genetic variant expressions, annotation, and filtering for great good.
ProteinToCodonTranslator
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