RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes

Abstract

9Recent advances in long-read sequencing have the potential to produce more complete genome 10 assemblies using sequence reads which can span repetitive regions. However, overlap based assembly 11 methods routinely used for this data require significant computing time and resources. Here, we have 12 developed RefKA, a reference-based approach for long read genome assembly. This approach relies on 13 breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with 14 PacBio reads, and then assembling each bin in parallel followed by a final bin-stitching step. During 15 benchmarking, we assembled the wheat Chinese Spring (CS) genome using publicly available PacBio 16 reads in parallel in 168 wall hours on a 250 CPU system. The maximum RAM used was 300 Gb and the 17 computing time was 42,000 CPU hours. The approach opens applications for the assembly of other 18 large and complex genomes with much-reduced computing requirements. The RefKA pipeline is

Chromosome‐level genome assembly of the bean bug Riptortus pedestris

“…De novo genome assembly was then performed using Canu (Koren et al, 2017) and Wtdbg2 (Ruan & Li, 2020) methods, respectively. Nextpolish was used to fix base errors in the genome using both long reads and short Illumina reads (Hu et al, 2020). The haploid genome was identified using HaploMerger2 (Huang et al, 2017) and purge haplotigs software program (Roach et al, 2018).…”

Chromosome-level genome assembly of the bean bug Riptortus pedestris

“…Correction was performed by Canu with the default parameters (Koren et al 2017). The resulting reads were assembled using SMARTdenovo (-k 21 -J 3000 -t 20) (Hu et al 2020). Nextpolish was used for genome polishing (Hu et al 2020).…”

“…The resulting reads were assembled using SMARTdenovo (-k 21 -J 3000 -t 20) (Hu et al 2020). Nextpolish was used for genome polishing (Hu et al 2020).…”