GraphBin2
☯️🧬 Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs (by metagentools)
kraken-biom
Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken). (by smdabdoub)
GraphBin2 | kraken-biom | |
---|---|---|
1 | 1 | |
27 | 43 | |
- | - | |
7.8 | 0.0 | |
10 days ago | about 2 years ago | |
Python | Python | |
BSD 3-clause "New" or "Revised" License | MIT License |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
GraphBin2
Posts with mentions or reviews of GraphBin2.
We have used some of these posts to build our list of alternatives
and similar projects.
kraken-biom
Posts with mentions or reviews of kraken-biom.
We have used some of these posts to build our list of alternatives
and similar projects.
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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?
When comparing GraphBin2 and kraken-biom you can also consider the following projects:
atlas - ATLAS - Three commands to start analyzing your metagenome data
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
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
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite
dada2 - Accurate sample inference from amplicon data with single nucleotide resolution
drep - Rapid comparison and dereplication of genomes
taxopedia - Taxonomic trees (cladograms) from Wikipedia-scraped data.