Abstract

The National Center for Biotechnology Information (NCBI) performs contamination screening of genome assemblies submitted to the archival GenBank. Advances in genome sequencing have accelerated the production of genome assemblies and their submission to public databases, necessitating high-performance screening tools. Since contaminants can lead to misleading conclusions about the biology of the organism in question (e.g. gene content, gene evolution, etc.), ideally contamination screening should be performed after the initial contig assembly and prior to downstream genome analyses.

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

• Are the sequences in a genome assembly contaminant-free?

Learning Objectives

• Learn how to screen a genome assembly for adaptor and vector contamination.
• Learn how to screen a genome assembly for non-host organism contamination.