Tigmint: correcting assembly errors using linked reads from large molecules

Abstract

BackgroundGenome sequencing yields the sequence of many short snippets of DNA (reads) from a genome. Genome assembly attempts to reconstruct the original genome from which these reads were derived. This task is difficult due to gaps and errors in the sequencing data, repetitive sequence in the underlying genome, and heterozygosity. As a result, assembly errors are common. In the absence of a reference genome, these misassemblies may be identified by comparing the sequencing data to the assembly and looking for discrepancies between the two. Once identified, these misassemblies may be corrected, improving the quality of the assembled sequence. Although tools exist to identify and correct misassemblies using Illumina paired-end and mate-pair sequencing, no such tool yet exists that makes use of the long distance information of the large molecules provided by linked reads, such as those offered by the 10x Genomics Chromium platform. We have developed the tool Tigmint to address this gap.ResultsTo demonstrate the effectiveness of Tigmint, we applied it to assemblies of a human genome using short reads assembled with ABySS 2.0 and other assemblers. Tigmint reduced the number of misassemblies identified by QUAST in the ABySS assembly by 216 (27%). While scaffolding with ARCS alone more than doubled the scaffold NGA50 of the assembly from 3 to 8 Mbp, the combination of Tigmint and ARCS improved the scaffold NGA50 of the assembly over five-fold to 16.4 Mbp. This notable improvement in contiguity highlights the utility of assembly correction in refining assemblies. We demonstrate the utility of Tigmint in correcting the assemblies of multiple tools, as well as in using Chromium reads to correct and scaffold assemblies of long single-molecule sequencing.ConclusionsScaffolding an assembly that has been corrected with Tigmint yields a final assembly that is both more correct and substantially more contiguous than an assembly that has not been corrected. Using single-molecule sequencing in combination with linked reads enables a genome sequence assembly that achieves both a high sequence contiguity as well as high scaffold contiguity, a feat not currently achievable with either technology alone.

Population sequencing enhances understanding of tea plant evolution

“…The final Hi-C-assisted genome assembly was commissioned by Annoroad Gene Technology. Tigmint (version 1.1.2) 53 was used to detect errors using linked reads from 10× Genomics Chromium. The reads were initially aligned to the Hi-C scaffolds, and the extents of the large DNA molecules were inferred from alignments of the reads.…”

Genomics of an avian neo-sex chromosome reveals the evolutionary dynamics of recombination suppression and sex-linked genes

“…After processing, 408 million read pairs remained with 95.6% whitelisted barcodes and a barcode diversity of 752,722. We used tigmint (Jackman et al 2018) with settings as=100, depth_treshold=65, minsize=2000, number of mismatches=5 to break contigs at suspected misassemblies and low-quality regions. Next, arcs (Yeo et al 2017) was used to scaffold the contigs using settings c = 5, e=30000 and r=0.05, followed by links v1.8.5 (also from the arcs pipeline)…”

Loss of genetic variation and sex determination system in North American northern pike characterized by whole-genome resequencing

“…In the second scaffolding stage, the Tigmint -arcs -links pipeline was utilized from BC Genome Sciences Centre. Tigmint v1.1.2 (Jackman et al, 2018) was run using the "arcs" pipeline to run all three stages. The Tigmint portion of the pipeline was run with default parameters.…”

“…First, Hi-C sequencing data was utilized with the SALSA2 pipeline (Ghurye et al, 2019) (Supplementary Figure 1) to generate an assembly with scaffold N50 of 18.8 Mbp across a total of 941 scaffolds. Second, 10X Chromium data was introduced with the Tigmint/ARCS pipeline (Jackman et al, 2018;Yeo et al, 2018), to both break suspect contigs and to further scaffold the genome. Error correction reduced contig N50 to 3.40 Mbp (1,395 contigs) while scaffold N50 increased to 23.3 Mbp.…”