GTDBTk
MMseqs2
| GTDBTk | MMseqs2 | |
|---|---|---|
| 1 | 4 | |
| 435 | 1,265 | |
| 4.4% | 1.9% | |
| 7.5 | 7.7 | |
| 16 days ago | 8 days ago | |
| Python | C | |
| GNU General Public License v3.0 only | GNU General Public License v3.0 only |
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GTDBTk
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Bacteria taxonomy determination!URGENT!
I would try GTDB-Tk, mOTUs2, or CAT/BAT
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).
CAT_pack - CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metagenomes
samtools - Tools (written in C using htslib) for manipulating next-generation sequencing data
dada2 - Accurate sample inference from amplicon data with single nucleotide resolution
hh-suite - Remote protein homology detection suite.
classify-genomes - Classify a genome sequence according to the mOTUs/specI taxonomy
SqueezeMeta - A complete pipeline for metagenomic analysis
bakta - Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
seqtk - Toolkit for processing sequences in FASTA/Q formats
pyani - Application and Python module for average nucleotide identity analyses of microbes.
htslib - C library for high-throughput sequencing data formats