MMseqs2
hh-suite
MMseqs2 | hh-suite | |
---|---|---|
5 | 2 | |
1,527 | 556 | |
1.6% | 0.7% | |
9.2 | 0.0 | |
15 days ago | 3 months ago | |
C | C | |
MIT License | GNU General Public License v3.0 only |
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MMseqs2
- Segmenting Credit Card Customers with K-Means: A Fun Dive into Clustering
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Clustering tool that could help cluster protein sequences based on percentage identity
A tool I often recommend for sequence clustering is mmseqs2 : https://github.com/soedinglab/MMseqs2, fast and efficient :)
- MMseqs2 – an example of great software for biology
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Metagenomics: abundances of short reads using genome databases
Tools like the the mmseqs2 "taxonomy" module, or DIAMOND v2, can efficiently align contigs to genome databases to assign taxonomy, but it seems like they aren't intended to provide abundance estimates for each taxon (since that would require mapping reads, and mmseqs2 can't even use paired-reads). Can anyone recommend tools or methods for A) connecting per-contig coverage information to contig taxonomy, or B) mapping short reads against genome databases?
- Retrieving One-to-One Orthologs of Unprocessed cDNAs
hh-suite
What are some alternatives?
htslib - C library for high-throughput sequencing data formats
foldseek - Foldseek enables fast and sensitive comparisons of large structure sets.
samtools - Tools (written in C using htslib) for manipulating next-generation sequencing data
MethylDackel - A (mostly) universal methylation extractor for BS-seq experiments.
SqueezeMeta - A complete pipeline for metagenomic analysis
direct-io - Direct IO helpers for block devices and regular files on FreeBSD, Linux, macOS and Windows.
seqtk - Toolkit for processing sequences in FASTA/Q formats
cglm - 📽 Highly Optimized 2D / 3D Graphics Math (glm) for C
kraken-biom - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
john - John the Ripper jumbo - advanced offline password cracker, which supports hundreds of hash and cipher types, and runs on many operating systems, CPUs, GPUs, and even some FPGAs
dada2 - Accurate sample inference from amplicon data with single nucleotide resolution
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.