Whole bacterial genome SNP analysis mapping reads to a reference genome
1. SNP analysis mapping reads to a reference genome
It consists in the SNP calling based on the mapping of the reads against a reference genome . Using this classical method you detect the SNPs aligning the reads from the genomes under analysis to the sequence of the reference genome.
The annotation used for evaluating the functional impact of the SNPs is the annotation of the reference genome.
You obtain a VCF file with the variants and a BAM file with its corresponding BAI file with the reads aligned to the reference. This approach allows to know the number of reads supporting each SNP.
2. SNP annotation to predict their functional impact
The filtering and evaluation of the impact of the variants is performed providing data of the location of the SNPs with respect to the annotated genes of the reference genome. This annotation of SNPs classifies the SNPs in different types with different functional impact: synonymous, missense, STOP gain, START loss, SNPs in a region with repetitive sequences or in a non coding region.
We provide a table with annotations for all the SNPs detected in all the genomes under analysis. This table allows us to do comparative analysis between the strains analyzed.
3. Phylogenetic analysis
A phylogenetic tree of the strains under analysis can be generated based on the SNPs detected in all the strains mapping their reads to the reference genome.
We provide the phylogenetic tree in different formats and in different types of visualization
SNP analysis for different types of project
This service fits in a wide range of project sizes: from large scale epidemiological projects for analyzing thousands of genomes to really specific projects focused on functional differences among a small set of strains of interest or even focused on only one strain.