This hub hosts assemblies of several Saccharomyces cerevisiae strains belonging to the Peterhof genetic collection and SNV tracks relative to the sacCer3 genome assembly.
Data for the following genomes are available at this page:
These tracks contain information about single nucleotide variations in several Saccharomyces cerevisiae strains of the Peterhof genetic collection as well as some other strains related to this project. For each strain, there are two separate tracks, one for substituions (SNV) and the other for short indels. For core strains of the collection, there are also tracks showing copy number variation.
SNV data are available for the following strains: 15V-P4, 25-25-2V-P3982, 1B-D1606, 74-D694, 6P-33G-D373, A1-K5-35B-D924, nm126-A1-K5-35B-D924, YPH499, and D273-10B.
This part of the hub shows assembly of the 15V-P4 strain, one of the progenitor strains for the whole collection.
This part shows assembly of the 25-25-2V-P3982 strain, a Peterhof strain with a long history of laboratory breeding.
This part of the hub features assembly of 1B-D1606, a hybrid strain descending to both Peterhof and S288C-related collections of yeast strains.
This part shows assembly of 74-D694, another hybrid strain, which has been widely used to study yeast prions.
This part of the hub collects (and allows one to compare) sets of annotations derived with different algorithms (listed as track names) as of May 2015. It is based on a slightly different assembly than the "final" 15V-P4 assembly, so contig names may be different. This work was done as a project in the Bioinformatics Institute http://bioinformaticsinstitute.ru/. For more information you might want to look here [Russian].
This part mostly serves educational purposes and is unlikely to be updated.
Genomes were assembled de novo with SPAdes v3.1 or v3.6 (applies to the 74-D694 genome only) and scaffolded with chromosomer. Comprehensive sets of genome annotations were created with Maker2.
For SNV analysis, short reads were aligned with bowtie v2.1.0; SNV calling was performed with samtools v1.0 mpileup. SNVs with quality less than 30 or DP less than 3, as well as heterozygous indels, were filtered out. The resulting files were annotated with SnpEff v4.1.
Contig naming conventions: NODE_int_int (number and ID). Scaffolds: I to XVI.
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