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57 changes: 57 additions & 0 deletions datasets/snpeff.yaml
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Name: SnpEff & SnpSift Genomic Variant Annotation Databases
Description: "SnpEff is a variant annotation and effect prediction tool that annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes). It supports over 38,000 genomes and provides comprehensive genomic databases for variant annotation. The databases include reference genomes, gene annotations, protein sequences, and regulatory elements from trusted sources like ENSEMBL, RefSeq, and UCSC. SnpSift complements SnpEff by providing tools to annotate genomic variants using databases, filter large genomic datasets, and manipulate annotated variants. Together, these tools provide a complete solution for genomic variant analysis, supporting research in human genetics, cancer genomics, pharmacogenomics, and model organism studies."
Contact: Pablo Cingolani <http://www.linkedin.com/in/pablocingolani>
Documentation: https://pcingola.github.io/SnpEff/
ManagedBy: "[Pablo Cingolani](http://www.linkedin.com/in/pablocingolani)"
UpdateFrequency: Monthly
Tags:
- snpeff
- life sciences
- genomic
- variant annotation
- bioinformatics
- genetic
- genome
- cancer
- protein
- vcf
- whole genome sequencing
- whole exome sequencing
- transcriptomics
- structural variation
License: "[MIT License](https://opensource.org/licenses/MIT)"
Resources:
- Description: "Pre-built genomic databases for many reference genomes including human (GRCh37, GRCh38), mouse, rat, and other model organisms. Each database contains gene annotations, transcript information, protein sequences, and regulatory elements required for variant annotation."
Type: S3 Bucket
DataAtWork:
Tutorials:
- Title: SnpEff Documentation
URL: https://pcingola.github.io/SnpEff/
AuthorName: Pablo Cingolani
AuthorURL: http://www.linkedin.com/in/pablocingolani
- Title: SnpEff Introduction and Quick Start
URL: https://pcingola.github.io/SnpEff/snpeff/introduction/
AuthorName: SnpEff Project
AuthorURL: https://pcingola.github.io/SnpEff/
- Title: Building Custom SnpEff Databases
URL: https://pcingola.github.io/SnpEff/snpeff/build_db/
AuthorName: SnpEff Project
AuthorURL: https://pcingola.github.io/SnpEff/
Tools & Applications:
- Title: SnpEff
URL: https://github.com/pcingola/SnpEff
AuthorName: Pablo Cingolani
AuthorURL: http://www.linkedin.com/in/pablocingolani
- Title: SnpSift
URL: https://github.com/pcingola/SnpSift
AuthorName: Pablo Cingolani
AuthorURL: http://www.linkedin.com/in/pablocingolani
Publications:
- Title: "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3"
URL: https://www.ncbi.nlm.nih.gov/pubmed/22728672
AuthorName: Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM
AuthorURL: https://www.ncbi.nlm.nih.gov/pubmed/?term=Cingolani%20P%5BAuthor%5D&cauthor=true&cauthor_uid=22728672
- Title: "Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift"
URL: https://www.frontiersin.org/articles/10.3389/fgene.2012.00035/full
AuthorName: Cingolani P, Patel VM, Coon M, Nguyen T, Land SJ, Ruden DM, Lu X
AuthorURL: https://www.frontiersin.org/people/u/4691