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Snippy Alternatives
Similar projects and alternatives to snippy based on common topics and language
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InfluxDB
Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.
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vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
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TileDB-VCF
Efficient variant-call data storage and retrieval library using the TileDB storage library.
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a better snippy alternative or higher similarity.
snippy reviews and mentions
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
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A note from our sponsor - SaaSHub
www.saashub.com | 25 Apr 2024
Stats
Basic snippy repo stats
6
436
3.9
6 months ago
tseemann/snippy is an open source project licensed under GNU General Public License v3.0 only which is an OSI approved license.
The primary programming language of snippy is Perl.
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