CoverM
Read coverage calculator for metagenomics (by wwood)
aviary
A hybrid assembly and MAG recovery pipeline (and more!) (by rhysnewell)
| CoverM | aviary | |
|---|---|---|
| 2 | 3 | |
| 253 | 67 | |
| - | - | |
| 6.8 | 9.0 | |
| about 2 months ago | 4 days ago | |
| Rust | Python | |
| GNU General Public License v3.0 only | GNU General Public License v3.0 only |
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.
CoverM
Posts with mentions or reviews of CoverM.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-06-12.
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what would you choose to detect specific genes in metagenomics data
(3) Depends on what you are trying to achieve. If you want number of reads mapping to the genes, either use DIAMOND BLASTX or map directly with Bowtie/minimap2 (or minimap2 through a package like CoverM).
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Filter out alignments that are less than 80% of the read length
I would recommend using CoverM
aviary
Posts with mentions or reviews of aviary.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-06-12.
-
what would you choose to detect specific genes in metagenomics data
Aviary is a good binning pipeline (there are others available), though perhaps more geared towards prokaryotes.
- Why bother reconstructing MAGs ?
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question about analysis of metagenome assembled genomes
Have a look at this especially the workflow figure https://github.com/rhysnewell/aviary
What are some alternatives?
When comparing CoverM and aviary you can also consider the following projects:
metaWRAP - MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
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
masurca
sv-callers - Snakemake-based workflow for detecting structural variants in genomic data