Subset selection of high-depth next generation sequencing reads for de novo genome assembly using MapReduce framework

Chih-Hao Fang, Yu-Jung Chang, Wei-Chun Chung, Ping-Heng Hsieh, Chung-Yen Lin, Jan-Ming Ho

Recent progress in next-generation sequencing technology has afforded several improvements such as ultra-high throughput at low cost, very high read quality, and substantially increased sequencing depth. State-of-the-art high-throughput sequencers, such as the Illumina MiSeq system, can generate ~15 Gbp sequencing data per run, with >80% bases above Q30 and a sequencing depth of up to several 1000x for small genomes. Illumina HiSeq 2500 is capable of generating up to 1 Tbp per run, with >80% bases above Q30 and often >100x sequencing depth for large genomes. To speed up otherwise time-consuming genome assembly and/or to obtain a skeleton of the assembly quickly for scaffolding or progressive assembly, methods for noise removal and reduction of redundancy in the original data, with almost equal or better assembly results, are worth studying. We developed two subset selection methods for single-end reads and a method for paired-end reads based on base quality scores and other read analytic tools using the MapReduce framework. We proposed two strategies to select reads: MinimalQ and ProductQ. MinimalQ selects reads with minimal base-quality above a threshold. ProductQ selects reads with probability of no incorrect base above a threshold. In the single-end experiments, we used Escherichia coli and Bacillus cereus datasets of MiSeq, Velvet assembler for genome assembly, and GAGE benchmark tools for result evaluation. In the paired-end experiments, we used the giant grouper (Epinephelus lanceolatus) dataset of HiSeq, ALLPATHS-LG genome assembler, and QUAST quality assessment tool for comparing genome assemblies of the original set and the subset. The results show that subset selection not only can speed up the genome assembly but also can produce substantially longer scaffolds. The software is freely available at https://github.com/moneycat/QReadSelector.