scoary-2
Calculate assocations between genes and traits (by MrTomRod)
bit
Bioinformatics Tools (by AstrobioMike)
scoary-2 | bit | |
---|---|---|
2 | 2 | |
14 | 81 | |
- | - | |
5.5 | 8.5 | |
2 months ago | 26 days ago | |
Python | Python | |
MIT License | 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.
scoary-2
Posts with mentions or reviews of scoary-2.
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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How can i build a phylogenetic tree from bacteria species taxids?
Turning the tree into a newick string can be done using a recursive function. Example: to_newick here: https://github.com/MrTomRod/scoary-2/blob/master/scoary/ScoaryTree.py
bit
Posts with mentions or reviews of bit.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-11-09.
-
How can i build a phylogenetic tree from bacteria species taxids?
The GtoTree dev has a fantastic parallelized downloader for assemblies: https://github.com/AstrobioMike/bit/blob/master/bit-dl-ncbi-assemblies
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I have a question about the FTP of annotation files from NCBI's Genbank and RefSeq
If you have the taxonomic IDs of your organisms of interest, there are existing parallelized download tools that are more efficient like https://github.com/kblin/ncbi-genome-download or bit-dl-ncbi-assemblies from https://github.com/AstrobioMike/bit
What are some alternatives?
When comparing scoary-2 and bit you can also consider the following projects:
Scoary - Pan-genome wide association studies
ncbi-genome-download - Scripts to download genomes from the NCBI FTP servers
GToTree - A user-friendly workflow for phylogenomics