Metabuli
MMseqs2
| Metabuli | MMseqs2 | |
|---|---|---|
| 1 | 4 | |
| 62 | 1,268 | |
| - | 2.6% | |
| 9.0 | 7.7 | |
| about 1 month ago | 7 days ago | |
| C++ | C | |
| GNU General Public License v3.0 only | GNU General Public License v3.0 only |
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Metabuli
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?
kraken-biom - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
samtools - Tools (written in C using htslib) for manipulating next-generation sequencing data
hh-suite - Remote protein homology detection suite.
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
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
MethylDackel - A (mostly) universal methylation extractor for BS-seq experiments.
samtools - [Moved to: https://github.com/ingolia/SamTools]
dada2 - Accurate sample inference from amplicon data with single nucleotide resolution
direct-io - Direct IO helpers for block devices and regular files on FreeBSD, Linux, macOS and Windows.