Snakemake pipeline for de novo genome assembly using a combination of long and short read sequencing data (ONT + 10x Illumina + HiFi PacBio Isoseq + Bionano OpticalMap)

Table of Contents

• Input data
• Linked reads Illumina (10x)
• Oxford Nanopore reads (ONT)

Input data

1. 10x Illumina: (a) set sample name in config.yaml (e.g. 'Her2'); (b) move 10x Illumina data in 10x/{sample} (e.g. 10x/Her2) directory

Linked reads Illumina (10x)

1. Performing supernova assembly of 10x data - assemble de novo genome (recommended 45-56x genome coverage)
2. Performing longranger basic pipeline - extracts and trims long-molecule barcodes
3. k-mer based genome metrics (fastq output of longrange basic)

Oxford Nanopore reads (ONT)