snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment (by tseemann)
TileDB-VCF
Efficient variant-call data storage and retrieval library using the TileDB storage library. (by TileDB-Inc)
| snippy | TileDB-VCF | |
|---|---|---|
| 6 | 4 | |
| 437 | 80 | |
| - | - | |
| 3.9 | 8.6 | |
| 7 months ago | 2 days ago | |
| Perl | C++ | |
| GNU General Public License v3.0 only | MIT License |
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.
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.
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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
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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?
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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).
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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
TileDB-VCF
Posts with mentions or reviews of TileDB-VCF.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-11-12.
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Has anyone stored/queried VCFs and their variant records in a relational database?
Perhaps of interest https://github.com/TileDB-Inc/TileDB-VCF
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[TileDB webinar] Population genomics is a data management problem
Here are the docs to the open-source TileDB-VCF storage engine: https://docs.tiledb.com/main/integrations-and-extensions/population-genomics
What are some alternatives?
When comparing snippy and TileDB-VCF you can also consider the following projects:
vcf2maf - Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
Hail - Cloud-native genomic dataframes and batch computing
dipcall - Reference-based variant calling pipeline for a pair of phased haplotype assemblies
gwas2vcf - Convert GWAS summary statistics to VCF
tronflow-vcf-postprocessing - A Nextflow variant normalization pipeline based on vt and bcftools
truvari - Structural variant toolkit for VCFs
RagTag - Tools for fast and flexible genome assembly scaffolding and improvement
Vcflib - C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
TileDB - The Universal Storage Engine
sgkit - We've moved to https://github.com/sgkit-dev/sgkit
gw - Genome browser and variant annotation
octopus - Bayesian haplotype-based mutation calling