hh-suite
MMseqs2
| hh-suite | MMseqs2 | |
|---|---|---|
| 2 | 4 | |
| 499 | 1,259 | |
| 1.8% | 1.9% | |
| 0.0 | 7.7 | |
| 9 months ago | 6 days ago | |
| C | C | |
| GNU General Public License v3.0 only | GNU General Public License v3.0 only |
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hh-suite
MMseqs2
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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
What are some alternatives?
foldseek - Foldseek enables fast and sensitive comparisons of large structure sets.
kraken-biom - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
MethylDackel - A (mostly) universal methylation extractor for BS-seq experiments.
samtools - Tools (written in C using htslib) for manipulating next-generation sequencing data
direct-io - Direct IO helpers for block devices and regular files on FreeBSD, Linux, macOS and Windows.
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
cglm - 📽 Highly Optimized 2D / 3D Graphics Math (glm) for C
SqueezeMeta - A complete pipeline for metagenomic analysis
seqtk - Toolkit for processing sequences in FASTA/Q formats
htslib - C library for high-throughput sequencing data formats
samtools - [Moved to: https://github.com/ingolia/SamTools]