kraken-biom
GraphBin2
| kraken-biom | GraphBin2 | |
|---|---|---|
| 1 | 1 | |
| 50 | 33 | |
| - | - | |
| 0.0 | 8.7 | |
| almost 3 years ago | 4 months ago | |
| Python | Python | |
| MIT License | BSD 3-clause "New" or "Revised" License |
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kraken-biom
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Differences between read based abundancy estimation programs? (metagenomics)
The issue is that after performing a taxonomic classification using kraken2, I want to create abundance tables regarding this taxonomic classification outputs. Some people have recommended me to use kraken--biom (https://github.com/smdabdoub/kraken-biom) and some others recommended me to use bracken (https://ccb.jhu.edu/software/bracken/index.shtml?t=manual).
GraphBin2
What are some alternatives?
atlas - ATLAS - Three commands to start analyzing your metagenome data
metaGEM - :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
dada2 - Accurate sample inference from amplicon data with single nucleotide resolution
drep - Rapid comparison and dereplication of genomes
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite
aviary - A hybrid assembly and MAG recovery pipeline (and more!)
abricate - :mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
taxopedia - Taxonomic trees (cladograms) from Wikipedia-scraped data.
flextaxd - FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )