In some research or clinical contexts it is not possible, or very hard, to purify DNA/RNA for sequencing from just the specimen of interest. Instead you will isolate DNA that is contaminated, sometimes heavily, with DNA/RNA of a different origin. This is the case for example with microbiome samples, which typically display considerable contamination with host DNA, or with samples of body fluids for pathogen detection. Such contamination can pose an issue with certain types of analyses, in particular with genome assembly.

This tutorial guides you through the preprocessing of sequencing data of bronchoalveolar lavage fluid (BALF) samples obtained from early COVID-19 patients in China. Since such samples are expected to be contaminated signficantly with human sequenced reads, the goal is to enrich the data for SARS-CoV-2 reads by identifying and discarding reads of human origin before trying to assemble the viral genome sequence.