RagTag
Tools for fast and flexible genome assembly scaffolding and improvement (by malonge)
snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment (by tseemann)
| RagTag | snippy | |
|---|---|---|
| 5 | 6 | |
| 431 | 437 | |
| - | - | |
| 0.0 | 3.9 | |
| 3 months ago | 7 months ago | |
| Python | Perl | |
| 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.
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.
-
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
-
how to improve denovo genome assembly with additional sequencing data.
Use ragtag. https://github.com/malonge/RagTag
-
Recommended tools for reference-guided genome assembly
RagTag. Not sure how well it works for small genomes.
-
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).
snippy
Posts with mentions or reviews of snippy.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-12-05.
-
Help/recommendations for whole genome sequence analysis
This should be of help, if you think you can get have a decent (closely related) reference genome from NCBI: https://github.com/tseemann/snippy
-
Software to automatically detect SNP's between 2 or more genomes?
snippy is a nice tool for this!
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Microbiome - would it be reasonable to assume that a bacterial contaminant (eg during library prep) would be the same isolate across contaminated samples?
So, let's say I have a batch of 20 samples, and I found evidence for my genus of interest in 5. What I've done is used Snippy (https://github.com/tseemann/snippy) with mapping based on a reference species in the genus. Snippy finds shared "core" regions of the reference species that are present in all samples and compares the SNPs between the samples. I find that each sample has distinct SNPs, which I believe indicates that the bacteria in each sample are not the same isolate. Thus, I am trying to argue that the bacteria could not have come from a shared contamination event during library prep. Does this make things more clear?
-
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).
-
Sorting reads to references with high identity
I would use snippy for this if there references are haploid genomes https://github.com/tseemann/snippy
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Inquiry regarding Snippy (by Seemann). My job has been running for more than 5 days with no update. Can anyone help me?
[18:37:12] Obtained from https://github.com/tseemann/snippy
What are some alternatives?
When comparing RagTag and snippy you can also consider the following projects:
scaffold-eth - 🏗 forkable Ethereum dev stack focused on fast product iterations
vcf2maf - Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
dr_scaffold - scaffold django rest apis like a champion 🚀
dipcall - Reference-based variant calling pipeline for a pair of phased haplotype assemblies
tronflow-vcf-postprocessing - A Nextflow variant normalization pipeline based on vt and bcftools
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
react-boilerplate - :fire: A highly scalable, offline-first foundation with the best developer experience and a focus on performance and best practices.
idba