drep
Rapid comparison and dereplication of genomes (by MrOlm)
covid-19-signal
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19. (by jaleezyy)
| drep | covid-19-signal | |
|---|---|---|
| 1 | 1 | |
| 237 | 30 | |
| - | - | |
| 3.9 | 5.5 | |
| about 2 months ago | about 1 month ago | |
| Python | Python | |
| - | 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.
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.
-
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.
covid-19-signal
Posts with mentions or reviews of covid-19-signal.
We have used some of these posts to build our list of alternatives
and similar projects.
-
What does a typical whole genome sequencing of SARS-CoV-2 fastq file look like?
For an example pipeline, check out SIGNAL - there is a workflow diagram in that repo https://github.com/jaleezyy/covid-19-signal
What are some alternatives?
When comparing drep and covid-19-signal you can also consider the following projects:
DAS_Tool - DAS Tool
16SMaRT - 16s rRNA Sequencing Meta-analysis Reproducibility Tool (using mothur).
SqueezeMeta - A complete pipeline for metagenomic analysis
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
kraken-biom - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
phantasm - PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes
masurca