GTDBTk
dada2
GTDBTk | dada2 | |
---|---|---|
1 | 1 | |
435 | 452 | |
4.4% | - | |
7.5 | 4.3 | |
16 days ago | 4 months ago | |
Python | R | |
GNU General Public License v3.0 only | GNU Lesser 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
dada2
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Error model generation and subsequent steps in DADA2 pipeline for multiple sequencing runs
It is recommended to process each run separately (https://github.com/benjjneb/dada2/issues/1177). Each flow cell behaves differently, so the error model for one might not work well for another run. You can merge them together once you have your sequence table.
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
TCGAbiolinks - TCGAbiolinks
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite
rBLAST - Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package
classify-genomes - Classify a genome sequence according to the mOTUs/specI taxonomy
MicrobiomeStat - Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
bakta - Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
pyani - Application and Python module for average nucleotide identity analyses of microbes.
phantasm - PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes