Referee: Reference assembly quality scores

Abstract

Genome assemblies from next-generation sequencing technologies are now an integral part of biological research, but many sequencing and assembly processes are still error-prone. Unfortunately, these errors can propagate to downstream analyses and wreak havoc on results and conclusions. Although such errors are recognized when dealing with diploid genotype data, modern reference assemblies (which are represented as haploid sequences) lack any type of succinct quality assessment for every position. Here we present Referee, a program that uses diploid genotype quality information in order to annotate a haploid assembly with a quality score for every position. Referee aims to provide an assembly with concise quality information on a Phred-like scale in FASTQ format for easy filtering of low-quality sites. Referee also provides output of quality scores in BED format that can be easily visualized as tracks on most genome browsers. Referee is freely available at https://gwct.github.io/referee/.