diamond
bwa-mem2
diamond | bwa-mem2 | |
---|---|---|
3 | 2 | |
969 | 685 | |
- | 2.2% | |
6.3 | 3.3 | |
3 months ago | 16 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?
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?
Biopython - Official git repository for Biopython (originally converted from CVS)
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
seqan3 - The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
bowtie2 - A fast and sensitive gapped read aligner
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
htslib - C library for high-throughput sequencing data formats
edlib - Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
vg - tools for working with genome variation graphs
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
GenomicSQLite - Genomics Extension for SQLite
seqstats - Quick summary statistics on fasta/fastq(.gz) files
IntaRNA - Efficient target prediction incorporating accessibility of interaction sites