Whole genome SNPs comparison: SNPtree, NDtree, CSI Phylogeny and kmer-based analysis

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Fausto Parisi
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1 Whole genome SNPs comparison: SNPtree, NDtree, CSI Phylogeny and kmer-based analysis Valeria Michelacci NGS course, June 2016

2 Webserver-based free pipelines available NCBI pipeline FDA GenomeTrakr CGE/DTU Batch upload and analysis Assembly (Annotation) Clustering based on SNPs analysis Storage at International Nucleotide Sequence Database Collaboration (INSDC) NCBI EMBL DDBJ Direct or after embargo period

3 Reference-based wgsnps typing Alignment to a reference sequence Compiling of a variant call format file per strain Compiling of a distance matrix Phylogenetic tree built on the distance matrix Tools available for download possibility to build your own pipeline CGE webserver hosted by DTU offers easy to use pipelines SNPs tree NDtree CSI phylogeny

4 Ref-based wgsnps/1: SNPs tree Leekitcharoenphon P, BMC Genomics 2012 = PFGE correlated isolates, Italy, August 2013 = not correlated isolates, Italy, August 2013 Analysis of all the detected nucleotidic differences based on the comparison with a reference sequence Epidemiologically related cases appear very different. Such a high sensitivity increases the risk for errors Discontinued on DTU CGE webserver

5 Ref-based wgsnps/2: NDtree Place Year SNPs analysis based on a different algorithm: only considering nucleotidic positions where the assigned nt is at least 10 times more represented than the other three More robust, less sensitive Epidemiologically related cases appear in the same cluster, but with no visible nucleotidic differences Very far strains appear with no differences The sensitivity may be too low Japan 2001 USA 1997 USA 1997 USA 2003 Italy 1989 Italy 2010 Joensen KG, JCM 2014

6 Ref-based wgsnps/3: CSI phylogeny Outbreak 1 (ST21) CSI phylogeny Outbreak 3 Kaas RS, Plos One 2014 It only computes positions having a good quality score in all the strains tested Outbreak 1bis (ST29) Only feed good sequences to avoid reducing the amount of computed positions! Outbreak 2 It accepts reads and/or contigs, but at least some samples need to be uploaded as reads to allow the computation of SNPs quality Epidemiological clusters identified, but no difference among strains

7 Reference-free wgsnps typing ksnp3 looks for SNPs in central positions of k-mers The optimal length of the kmer is computed for every batch of test sequences It accepts fasta files Different clustering algorithms available Available for download as a tool package operated via command line Available on ARIES (

8 Ref-free wgsnps typing: ksnp3 (through ARIES) Gardner SN, Bioinformatics Outbreak Outbreak Outbreak 1 (ST21) O26 eae- stx- Epidemiological clusters correctly identified Intra-cluster discrimination Outbreak 1bis (ST29)

9 ksnp3 ARIES: how does it work? E. coli typing - phylogeny MakeKSNP3infile MakeFasta Kchooser It identifies an optimum value of k for your specific data set ksnp Flag the options for estimating Neighbor Joining and maximum likelihood trees

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