Personal genome analysis software tools | Genome annotation
Individuals are now empowered to obtain and explore their full personal genome and exome sequences owing to declining costs in genome sequencing, and direct-to-consumer genetic testing companies have begun to provide sequencing services: in 2011, 23andMe conducted a pilot exome sequencing program for $999, while at the time of this writing, DNADTC provides the service for $895.
Allows visualization and sharing of next-generation sequencing (NGS) data. GBrowse is a web-based genome browser divided between code that runs on the web server and on the web browser client. The software is suitable for installation on public web sites, as well as the web sites of small-to medium collaborations among several geographically separate groups. It also integrates well with the other bioinformatics tools in the Generic Model Organism Database (GMOD) suite.
A python package that allows you to easily combine reference genomes and sets of polymorphisms together to create personalized genomes. Personalized genomes can be used to work directly on the genomes of you subjects and be translated into personalized proteomes. Multiple sets of polymorphisms can also be combined together to leverage their independent benefits. Ex: RNA-seq and DNA-seq for the same individual to improve the coverage, RNA-seq of an individual + dbSNP for validation, Combine the results of RNA-seq of several individuals to create a genome only containing the common polymorphisms. pyGeno is also a personal database that give you access to all the information provided by Ensembl (for both reference and personalized genomes) without the need of queries to distant HTTP APIs. It also comes with parsers for several file types and various other useful tools.
A literature retrieval system that builds a personal DNA report based on the scientific literature cited in SNPedia and a file of genotype (DNA) data. Customers of DNA testing services (23andMe, FamilyTreeDNA, Ancestry.com, Complete Genomics, ...) can use it to retrieve published data about their DNA completely independent of whichever company produced the data.
A simple light-weight distributed annotation system (DAS) tool for visualization of genomic annotation. myKaryoView has been specifically configured to help analyse data derived from personal genomics, although it can also be used as a generic genome browser visualization. Several well-known data sources are provided to facilitate comparison of known genes and normal variation regions. The navigation experience is enhanced by simultaneous rendering of different levels of detail across chromosomes. A simple interface is provided to allow searches for any SNP, gene or chromosomal region.
Interprets genotype without compromising privacy. Interpretome doesn’t store personal genotype data that stay on computer’s and browser’s users. This software allows single nucleotide polymorphism (SNP) annotations and enables the sharing of these genomic annotations. Users can also share analysis results for personal genome exploration.
A methodology for federated analysis of sequence variants from personal genomes. The key concept in NGS-Logistics is to let users query SNVs across data sets in multiple centers. Users get a full description of the results for the samples to which they have authorized access, while getting relevant summary information for other samples. This summary information is sufficient to carry out key research tasks, such as identifying relevant mutations in a patient population. The footprint on personal genomic data from other patients is kept to a bare minimum.
A graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.