taxopedia
kraken-biom
| taxopedia | kraken-biom | |
|---|---|---|
| 4 | 1 | |
| 7 | 47 | |
| - | - | |
| 0.0 | 0.0 | |
| almost 3 years ago | over 2 years ago | |
| Python | Python | |
| MIT License | MIT License |
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taxopedia
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).
What are some alternatives?
graphlan - High-quality circular representations of taxonomic and phylogenetic trees
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
ielex-data-and-tree - Data and scripts for producing a Baysian phylogenetic tree sample of for the Indo-European family which is "good enough", using data from IELex (Dunn et al. 2011).
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite
Wikipedia-API - Python wrapper for Wikipedia
atlas - ATLAS - Three commands to start analyzing your metagenome data
Wikipedia-Article-Scraper - A complete Python text analytics package that allows users to search for a Wikipedia article, scrape it, conduct basic text analytics and integrate it to a data pipeline without writing excessive code.
dada2 - Accurate sample inference from amplicon data with single nucleotide resolution
drep - Rapid comparison and dereplication of genomes
GraphBin2 - ☯️🧬 Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs
Metabuli - Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.