Scoary
Pan-genome wide association studies (by AdmiralenOla)
sgkit
We've moved to https://github.com/sgkit-dev/sgkit (by pystatgen)
Scoary | sgkit | |
---|---|---|
2 | 1 | |
137 | 0 | |
- | - | |
10.0 | 5.9 | |
over 1 year ago | about 2 months ago | |
Python | HTML | |
GNU General Public License v3.0 only | Apache License 2.0 |
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.
Scoary
Posts with mentions or reviews of Scoary.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-11-28.
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Functional pangenome analysis using Roary strategy?
How about mGWAS, such as Scoary or my about-to-be-published successor Scoary2?
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Is Unicycler the best option for hybrid genome assembly?
BONUS: I was planning on using Scoary (https://github.com/AdmiralenOla/Scoary) together with some Virulence data I have to look for some candidates. Any suggestion of alternative ways to identify virulence factors in these genomes?
sgkit
Posts with mentions or reviews of sgkit.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-11-12.
-
Has anyone stored/queried VCFs and their variant records in a relational database?
I once built on top of a library that used the zarr format for storing the vcf data. It allowed me to parse over it like it was a pandas dataframe and incredibly fast. sgkit is the successor library and seems to be growing really well, but I haven't played with it. I do have high hopes for the zarr format, but I am biased
What are some alternatives?
When comparing Scoary and sgkit you can also consider the following projects:
plassembler - Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
TileDB-VCF - Efficient variant-call data storage and retrieval library using the TileDB storage library.
scoary-2 - Calculate assocations between genes and traits
Dask - Parallel computing with task scheduling
merqury - k-mer based assembly evaluation
gwas2vcf - Convert GWAS summary statistics to VCF
Perfect-bacterial-genome-tutorial
Hail - Cloud-native genomic dataframes and batch computing