drep
kraken-biom
| drep | kraken-biom | |
|---|---|---|
| 1 | 1 | |
| 237 | 43 | |
| - | - | |
| 3.9 | 0.0 | |
| about 2 months ago | about 2 years ago | |
| Python | Python | |
| - | MIT License |
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drep
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How to dereplicate MAGs? (metagenome assembly genomes)
You should look at https://github.com/MrOlm/drep . Thats exactly the tool you need. Usually one takes all their bins and dereplicates them at 99% ANI for strain level dereplication or 95% at species level. For preserving the best quality, you would need to check yourself if the best genome survived the dereplication afaik. You probably want some sort of quality score and chose the one with the highest score out of the bins that got grouped as one by dereplication.
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?
DAS_Tool - DAS Tool
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
SqueezeMeta - A complete pipeline for metagenomic analysis
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite
covid-19-signal - Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
atlas - ATLAS - Three commands to start analyzing your metagenome data
phantasm - PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes
dada2 - Accurate sample inference from amplicon data with single nucleotide resolution
masurca
GraphBin2 - ☯️🧬 Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs
taxopedia - Taxonomic trees (cladograms) from Wikipedia-scraped data.