Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information

Abstract

BackgroundLong DNA reads produced by single molecule and pore-based sequencers are more suitable for assembly and structural variation discovery than short read DNA fragments. For de novo assembly, PacBio and Oxford Nanopore Technologies (ONT) are favorite options. However, PacBio’s SMRT sequencing is expensive for a full human genome assembly and costs over 40,000 USD for 30x coverage as of 2019. ONT PromethION sequencing, on the other hand, is one-twelfth the price of PacBio for the same coverage. This study aimed to compare the cost-effectiveness of ONT PromethION and PacBio’s SMRT sequencing in relation to the quality.FindingsWe performed whole genome de novo assemblies and comparison to construct an improved version of KOREF, the Korean reference genome, using sequencing data produced by PromethION and PacBio. With PromethION, an assembly using sequenced reads with 64x coverage (193 Gb, 3 flowcell sequencing) resulted in 3,725 contigs with N50s of 16.7 Mbp and a total genome length of 2.8 Gbp. It was comparable to a KOREF assembly constructed using PacBio at 62x coverage (188 Gbp, 2,695 contigs and N50s of 17.9 Mbp). When we applied Hi-C-derived long-range mapping data, an even higher quality assembly for the 64x coverage was achieved, resulting in 3,179 scaffolds with an N50 of 56.4 Mbp.ConclusionThe pore-based PromethION approach provides a good quality chromosome-scale human genome assembly at a low cost with long maximum contig and scaffold lengths and is more cost-effective than PacBio at comparable quality measurements.

Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing

“…Those developed by ONT can be found on their github page (https://github .com/nanoporetech). Available tools, among others, include medaka, tombo, pomoxis, and nanopolish, which are used for sequence correction, identifying modified nucleotides from raw sequencing data, genome assembly, and error correction in genomic assemblies, respectively (39)(40)(41)(42).…”

BiSCoT: improving large eukaryotic genome assemblies with optical maps

“…However, a high proportion of them are still fragmented and few represent the chromosome organization of the genome. Recently, long reads sequencing techniques, like Oxford Nanopore Technologies and Pacific Biosciences, were introduced to improve the contiguity of assemblies, by sequencing DNA molecules that can range from a few kilobases to more than a megabase in size ( Istace et al, 2017 ; Schmidt et al, 2017 ; Kim et al, 2019 ; Shafin et al, 2019 ). Nevertheless and even if the assemblies were greatly improved, the chromosome-level organization of the sequenced genome cannot be deciphered in a majority of cases.…”

Peer Review #1 of "BiSCoT: improving large eukaryotic genome assemblies with optical maps (v0.1)"

“…However, a high proportion of them are still fragmented and few represent the chromosome organization of the genome. Recently, long reads sequencing techniques, like Oxford Nanopore Technologies and Pacific Biosciences, were introduced to improve the contiguity of assemblies, by sequencing DNA molecules that can range from a few kilobases to more than a megabase in size (Istace et al (2017); Schmidt et al (2017); Kim et al (2019); Shafin et al (2019)). Nevertheless and even if the assemblies were greatly improved, the chromosome-level organization of the sequenced genome cannot be deciphered in a majority of cases.…”