phantasm
PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes (by dr-joe-wirth)
drep
Rapid comparison and dereplication of genomes (by MrOlm)
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.
phantasm
Posts with mentions or reviews of phantasm.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-04-02.
- Is there any way to easily create a docker image that has both python and R?
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PHANTASM: new software for microbial taxonomy
The easiest way to try it out PHANTASM is to use the Docker image. The source code is also available on github.
drep
Posts with mentions or reviews of drep.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-07-25.
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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.
What are some alternatives?
When comparing phantasm and drep you can also consider the following projects:
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
DAS_Tool - DAS Tool
pyani - Application and Python module for average nucleotide identity analyses of microbes.
kraken-biom - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
misp-taxonomies - Taxonomies used in MISP taxonomy system and can be used by other information sharing tool.
masurca