Any advice on aneuploidies and CNVs in R or python using Illumina reads?

10 October 2015 1 5K Report

Hi,

I'm looking for a pipeline for R or python where I can use a Reference genome as fasta format and map my Illumina reads in fastq to get a chromosome representation from where I can figure out for the presence of aneuploidies or insertion/deletion regions.

I'm working with yeast genome sequences.

Thanks.

Galo Adrián Goig

I think you could map your sequences against a reference using any aligner like BWA and then visualize the alignment with integrative genome viewer (IGV).

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