diamond
minimap2
| diamond | minimap2 | |
|---|---|---|
| 3 | 5 | |
| 969 | 1,698 | |
| - | - | |
| 6.3 | 7.6 | |
| 3 months ago | 6 days ago | |
| C++ | C | |
| GNU General Public License v3.0 only | GNU General Public License v3.0 or later |
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diamond
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comparing the similarity between a set of protein sequences
Diamond (https://github.com/bbuchfink/diamond) might help. It has a protein sequence clustering option. You could cluster your sequences and then take the centroids of each cluster. Vary the BLAST parameters to increase/decrease the numbers of clusters.
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which database is best to use on BLAST to identify an unknown protein?
What I usually do is the DIAMOND search (https://github.com/bbuchfink/diamond) on UniRef (50/90) database.
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someone remotely helped me to download and execute this file called a diamond.exe from the following link: https://github.com/bbuchfink/diamond Windows said it could be unsafe so I disabled Windows Defender and pressed run on it but it didn't do anything, is this a virus is it safe?
someone remotely helped me to download and execute this file called a diamond.exe from the following link: https://github.com/bbuchfink/diamond Windows said it could be unsafe so I disabled Windows Defender and pressed run on it but it didn't do anything, is this a virus is it safe?
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?
Biopython - Official git repository for Biopython (originally converted from CVS)
bwa-mem2 - The next version of bwa-mem
seqan3 - The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
seqtk - Toolkit for processing sequences in FASTA/Q formats
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
miniprot - Align proteins to genomes with splicing and frameshift