GTDBTk
phantasm
GTDBTk | phantasm | |
---|---|---|
1 | 2 | |
495 | 23 | |
1.4% | - | |
6.7 | 8.6 | |
2 months ago | about 1 year ago | |
Python | Python | |
GNU General Public License v3.0 only | MIT License |
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GTDBTk
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Bacteria taxonomy determination!URGENT!
I would try GTDB-Tk, mOTUs2, or CAT/BAT
phantasm
- Is there any way to easily create a docker image that has both python and R?
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PHANTASM: new software for microbial taxonomy
The easiest way to try it out PHANTASM is to use the Docker image. The source code is also available on github.
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).
pyani - Application and Python module for average nucleotide identity analyses of microbes.
dada2 - Accurate sample inference from amplicon data with single nucleotide resolution
drep - Rapid comparison and dereplication of genomes
bakta - Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
misp-taxonomies - Taxonomies used in MISP taxonomy system and can be used by other information sharing tool.
CAT_pack - CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metagenomes
seurat-docker - Docker images of Seurat
classify-genomes - Classify a genome sequence according to the mOTUs/specI taxonomy
pyGenomeViz - A genome visualization python package for comparative genomics
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite