Prevention, diagnosis, and treatment of high-throughput sequencing data pathologies

High Throughput Sequencing (HTS) technologies generate millions of sequence reads from DNA/RNA molecules rapidly and cost-effectively, enabling single investigator laboratories to address a variety of “omics” questions in non-model organisms, fundamentally changing the way genomic approaches are used to advance biological research. One major challenge posed by HTS is the complexity and difficulty of data quality control (QC). While QC issues associated with sample isolation, library preparation, and sequencing are well known and protocols for their handling are widely available, the QC of the actual sequence reads generated by HTS is often overlooked. HTS-generated sequence reads can contain various errors, biases, and artefacts whose identification and amelioration can greatly impact subsequent data analysis. However, a systematic survey on QC procedures for HTS data is still lacking. In this review, we begin by presenting standard “health check-up” QC procedures recommended for HTS da...