SNPsites

The SNPsites plugin for isolate databases will create alignments for each selected locus for the set of isolates chosen. These alignments are then passed to the snp-sites tool. which will generate VCF files for each locus. A summary table will be created showing the number of alleles and polymorphisms found for each locus.

The snp-sites algorithm and program are described in Page et al. 2016. Microb Gen 2:e000056.

The function can be accessed by selecting the ‘Analysis’ section on the main contents page.

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Jump to the ‘Analysis’ category, follow the link to ‘SNPSites’, then click ‘Launch SNPsites’.

Alternatively, it can be accessed following a query by clicking the ‘SNPSites’ button in the Analysis list at the bottom of the results table. Please note that the list of functions here may vary depending on the setup of the database.

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Enter the ids of the isolate records to analyse - these will be already entered if you accessed the plugin following a query. Select the loci you would like to analyse, either from the dropdown loci list, and/or by selecting one or more schemes.

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Click submit. The job will be submitted to the queue and will start running shortly.

Output consists of a summary file showing the number of sequences found in the dataset, the number of unique alleles, and the number of SNPs for each locus. An interactive chart is also displayed showing these values. Finally, Zip files are produced that contain FASTA alignments and VCF files for each locus.

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