MMseqs2
GTDBTk
| MMseqs2 | GTDBTk | |
|---|---|---|
| 4 | 1 | |
| 1,265 | 435 | |
| 2.4% | 4.8% | |
| 7.7 | 7.5 | |
| 13 days ago | 21 days ago | |
| C | Python | |
| GNU General Public License v3.0 only | GNU General Public License v3.0 only |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
MMseqs2
-
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
-
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
GTDBTk
-
Bacteria taxonomy determination!URGENT!
I would try GTDB-Tk, mOTUs2, or CAT/BAT
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
CAT_pack - CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metagenomes
hh-suite - Remote protein homology detection suite.
dada2 - Accurate sample inference from amplicon data with single nucleotide resolution
SqueezeMeta - A complete pipeline for metagenomic analysis
classify-genomes - Classify a genome sequence according to the mOTUs/specI taxonomy
seqtk - Toolkit for processing sequences in FASTA/Q formats
bakta - Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
htslib - C library for high-throughput sequencing data formats
pyani - Application and Python module for average nucleotide identity analyses of microbes.