LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly

Abstract

BackgroundCompleting a genome is an important goal of genome assembly. However, many assemblies, including reference assemblies, are unfinished and have a number of gaps. Long reads obtained from third-generation sequencing (TGS) platforms can help close these gaps and improve assembly contiguity. However, current gap-closure approaches using long reads require extensive runtime and high memory usage. Thus, a fast and memory-efficient approach using long reads is needed to obtain complete genomes.FindingsWe developed LR_Gapcloser to rapidly and efficiently close the gaps in genome assembly. This tool utilizes long reads generated from TGS sequencing platforms. Tested on de novo assembled gaps, repeat-derived gaps, and real gaps, LR_Gapcloser closed a higher number of gaps faster and with a lower error rate and a much lower memory usage than two existing, state-of-the art tools. This tool utilized raw reads to fill more gaps than when using error-corrected reads. It is applicable to gaps in the assemblies by different approaches and from large and complex genomes. After performing gap-closure using this tool, the contig N50 size of the human CHM1 genome was improved from 143 kb to 19 Mb, a 132-fold increase. We also closed the gaps in the Triticum urartu genome, a large genome rich in repeats; the contig N50 size was increased by 40%. Further, we evaluated the contiguity and correctness of six hybrid assembly strategies by combining the optimal TGS-based and next-generation sequencing-based assemblers with LR_Gapcloser. A proposed and optimal hybrid strategy generated a new human CHM1 genome assembly with marked contiguity. The contig N50 value was greater than 28 Mb, which is larger than previous non-reference assemblies of the diploid human genome.ConclusionsLR_Gapcloser is a fast and efficient tool that can be used to close gaps and improve the contiguity of genome assemblies. A proposed hybrid assembly including this tool promises reference-grade assemblies. The software is available at http://www.fishbrowser.org/software/LR_Gapcloser/.

Genomic balancing selection is key to the invasive success of the fall armyworm

“…If an error is found over a gap, the scaffold was broken into two using the same software to remove potential structural errors in the assembly. The broken assemblies were concatenated using SALSA2 60 or 3D-DNA 61 , followed by gap filling with the 80X Illumina reads using SOAP-denovo2 Gap-Closer 62 and with the PacBio reads using LR_GapCloser v1.1 63 . We observed that 3D-DNA generated a slightly more correct assembly than SALSA2 from BUSCO analysis (Table S1).…”

Improved contiguity of the threespine stickleback genome using long-read sequencing

“…This assembly had a total of 3593 contigs (N50: 683 kb) from across the genome. We closed gaps in the v. 4 threespine stickleback reference assembly using these contigs and LR_Gapcloser with the parameter -a 1 (Xu et al 2019). We increased the allowed deviation between gap length and the inserted sequence length in order to provide additional flexibility for gap size that was not inferred accurately in the v. 4 genome assembly.…”

Improved Reference Genome forCyclotella CrypticaCCMP332, a Model for Cell Wall Morphogenesis, Salinity Adaptation, and Lipid Production in Diatoms (Bacillariophyta)

“…8 We scaffolded the polished contigs using the corrected nanopore sequences with SSPACE-LongRead (version 1-1) (Boetzer and Pirovano 2014), requiring three overlaps to connect contigs ('-l 3'). We used the corrected nanopore reads to extend contigs and fill scaffold gaps using LR_Gapcloser (Xu et al 2019) with default settings and a total of ten iterative rounds. Finally, we aligned the corrected nanopore reads to the scaffolds with Minimap2 and used these alignments to remove redundant scaffolds from the assembly using Purge Haplotigs (version 1.0.0) (Roach et al 2018).…”