Snippy-core
Introduction
The Snippy-core analysis includes a Snippy run (Rapid haploid variant calling and core genome alignment), which aligns the selected samples to a reference in .gb format, and Snippy-core (hence the name) to merge Snippy's VCFs into a core.vcf file, finding core variants (SNPs e indels common to all samples).
Snippy & Snippy-core GitHub Page: https://github.com/tseemann/snippy
Run Analysis Snippy-core
Once the analysis Snippy-core has been selected from the run analyses interface, the wizard will present a confirmation UI. The analysis is specific for Snippy+Snippy-core and there are no other available tools.
The input selection wizard will require selection of a .gb reference for Snippy-core execution, after Snippy.
The input selection wizard delivers an advanced input selection mode, to allow selection of all types of supported input files at once.
Accepted inputs can be from:
A link to Check analysis will be created after launching the requested analysis. The system will notify the user after a succesful analysis launch and once execution has ended.
Output directory
Please refer to Cohesive's specific Wiki page for information on file download.
The output directory can be reached from the link of the download page or from the link in the analysis summary. The results directory is located directly in the root directory and it contains the following 2 directories:
- meta: ("metadata") contains log and configuration files.
- result: contains the analysis' output files.
The table below lists files available in the output directory structure, alongside some useful information.
| File | Description | Location |
|---|---|---|
| core.aln | fasta file with sequences from samples and from reference | result directory |
| core.full.aln | fasta file with samples' sequences aligned to the reference's | result directory |
| core.ref.fa | fasta file with the reference genome's nucleotide sequence | result directory |
| core.tab | tsv variants table. Columns: Chromosome, position, nucleotide in reference, nucleotide in sample 1, nucleotide in sample 2... | result directory |
| core.txt | text file with summary table of sample and reference sequence features | result directory |
| core.vcf | VCFv4.2 variants file. Includes an informative header and the table listing variant type and vairant presence/absence binary matrix for samples | result directory |
