MMseqs2
hh-suite
| MMseqs2 | hh-suite | |
|---|---|---|
| 4 | 2 | |
| 1,265 | 501 | |
| 2.4% | 2.2% | |
| 7.7 | 0.0 | |
| 14 days ago | 9 months ago | |
| C | C | |
| GNU General Public License v3.0 only | GNU General Public License v3.0 only |
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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
hh-suite
What are some alternatives?
kraken-biom - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
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.
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
direct-io - Direct IO helpers for block devices and regular files on FreeBSD, Linux, macOS and Windows.
SqueezeMeta - A complete pipeline for metagenomic analysis
cglm - 📽 Highly Optimized 2D / 3D Graphics Math (glm) for C
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]