SVMU analysis using short read contigs.

[koushik1989]

Dear Mahul, I intend to use SVMU for calling variants between a reference and a newly sequenced strain of Drosophila. I have the contigs and also a scaffolded assembly for the same built from Illumina short reads. Can I proceed with my short read assembly? I also have a pseudo-chromosomes built using mscaffolder, can I use this as query. My current strategy is using pseudo-chromosomes I built using mscaffolder as a query. I am able to run the analysis successfully. I need your inputs pertaining to my workflow. Hoping for a positive response. Thank you

[mahulchak]

Hi Koushik, Feel free to try svmu on the pseudoscaffolds and let me know what you get.

On Mon, Mar 16, 2020, 06:17 koushik1989 [email protected] wrote:

Dear Mahul, I intend to use SVMU for calling variants between a reference and a newly sequenced strain of Drosophila. I have the contigs and also a scaffolded assembly for the same built from Illumina short reads. Can I proceed with my short read assembly? I also have a pseudo-chromosomes built using mscaffolder, can I use this as query. My current strategy is using pseudo-chromosomes I built using mscaffolder as a query. I am able to run the analysis successfully. I need your inputs pertaining to my workflow. Hoping for a positive response. Thank you

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