BACTERIA ORGANISM WITH TWO CHROMOSOMES

[vappiah]

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]

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]

Thanks @stevendavis

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

[hughrandFDA]

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 From: Steve Davis ***@***.***> Sent: Tuesday, March 16, 2021 11:11 AM To: CFSAN-Biostatistics/snp-pipeline ***@***.***> Cc: Subscribed ***@***.***> Subject: [EXTERNAL] Re: [CFSAN-Biostatistics/snp-pipeline] BACTERIA ORGANISM WITH TWO CHROMOSOMES (#20) CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. 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. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#20 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AB2BAG5O3ODFK7JLBA3CIH3TD5YJRANCNFSM4ZIOD7OQ>.

[vappiah]

Thanks everyone for your comments.