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CFSAN-Biostatistics / snp-pipeline

SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.
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BACTERIA ORGANISM WITH TWO CHROMOSOMES #20

Closed vappiah closed 3 years ago

vappiah commented 3 years ago

Hello CFSAN developers,

I like to use CFSAN to identify snps in _Vibrio _cholerae__ isolates. But the each isolate has two chromosomes, meaning to reference sequences. Is it possible to run CFSAN by specifying two reference genomes ? Please advice and thanks in advance.

stevendavis commented 3 years ago

Your use-case is not something we have attempted. The CFSAN snp pipeline can only accept a single reference file. The reference can have multiple contigs. You might consider combining the two chromosomes into a single fasta file. YMMV.

vappiah commented 3 years ago

Thanks @stevendavis

Another strategy I want to use is to call snps using chromosome1 and 2 in seperate files.

hughrandFDA commented 3 years ago

Concatenating the two chromosomes should work reasonably well. I don’t have experience with Vibrio, but my understanding is that it’s genome is fairly dynamic - that may cause you more trouble than having to deal with two chromosomes. And keep in mind that reference-based analyses are best suited for isolates that are fairly close evolutionarily.

Hugh

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Your use-case is not something we have attempted. The CFSAN snp pipeline can only accept a single reference file. The reference can have multiple contigs. You might consider combining the two chromosomes into a single fasta file. YMMV.

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vappiah commented 3 years ago

Thanks everyone for your comments.