By: Blogs on jonathanBieler.github.io

Re-posted from: https://jonathanbieler.github.io/blog/fastq2cnv/

I’ve recently worked on Julia bindings for BWA, allowing to align sequencing reads (FASTA or FASTQ) to a reference genome directly from Julia. On top of this, updates to XAM.jl and BioRecordsProcessing.jl will make it possible to build end-to-end workflows in Julia, from raw reads to analysis results.
To illustrate this I will showcase online whole-genome sequencing (WGS) copy number variation (CNV) calling on a mouse kidney tumor sample.
Briefly, we need to do the following :