RagTag
Tools for fast and flexible genome assembly scaffolding and improvement (by malonge)
idba
By loneknightpy
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.
RagTag
Posts with mentions or reviews of RagTag.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-05-01.
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Bacterial reference-guided assembly vs. de-novo assembly unicycler?
Has anyone used ragtag to correct bacterial assemblies (https://github.com/malonge/RagTag/wiki/correct) ? Is it helpful?
- Question about genome assembly tools
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how to improve denovo genome assembly with additional sequencing data.
Use ragtag. https://github.com/malonge/RagTag
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Recommended tools for reference-guided genome assembly
RagTag. Not sure how well it works for small genomes.
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How to find sequence variations from contigs
My first idea was to assemble the contigs into scaffolds (e. g. using RagTag) and then look for a tool that can identify these mutations. However, I've also come across snippy, which is a tool that can identify mutations from reads. I don't know if I can just apply it to contigs though (probably not).
idba
Posts with mentions or reviews of idba.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-05-01.
-
Bacterial reference-guided assembly vs. de-novo assembly unicycler?
I de-novo assembled the short reads with unicycler and produced a phylogenetic tree with all 35 genomes. I am planning to use https://github.com/loneknightpy/idba to re-assemble the short reads using their corresponding most closely related "perfect" genome as a reference.
What are some alternatives?
When comparing RagTag and idba you can also consider the following projects:
scaffold-eth - 🏗 forkable Ethereum dev stack focused on fast product iterations
dr_scaffold - scaffold django rest apis like a champion 🚀
dipcall - Reference-based variant calling pipeline for a pair of phased haplotype assemblies
DIF - "DNA IMAGE FOOTPRINT" The main idea is to convert a DNA sequence to an image to find any related sequences in the image with common algorithms
snippy - :scissors: :zap: Rapid haploid variant calling and core genome alignment
react-boilerplate - :fire: A highly scalable, offline-first foundation with the best developer experience and a focus on performance and best practices.