TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads

Xu, Mengyang; Guo, Lidong; Gu, Shengqiang; Wang, Ou; Zhang, Rui; Peters, Brock A.; Fan, Guangyi; Liu, Xin; Xu, Xun; Deng, Li; Zhang, Yong‐Wei

doi:10.1093/gigascience/giaa094

Cited by 244 publications

(174 citation statements)

References 46 publications

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“…De novo assembly was performed by Supernova v2.1.1 (Supernova assembler, RRID:SCR_016756 ) [ 44 ] using the suggested parameters (--maxreads=2100000000 --accept-extreme-coverage --nopreflight). TGS-GapCloser v1.0.0 (TGS-GapCloser, RRID:SCR_017633 ) [ 45 , 46 ] was used to fill the gaps between contigs within same scaffolds, and this process was performed under the use of error-corrected ONT or PacBio data by Canu. The number of gaps within scaffolds was computed using the formula: number of contigs − number of scaffolds.…”

Section: Methodsmentioning

confidence: 99%

Comparison of long-read methods for sequencing and assembly of a plant genome

et al. 2020

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Background Sequencing technologies have advanced to the point where it is possible to generate high-accuracy, haplotype-resolved, chromosome-scale assemblies. Several long-read sequencing technologies are available, and a growing number of algorithms have been developed to assemble the reads generated by those technologies. When starting a new genome project, it is therefore challenging to select the most cost-effective sequencing technology, as well as the most appropriate software for assembly and polishing. It is thus important to benchmark different approaches applied to the same sample. Results Here, we report a comparison of 3 long-read sequencing technologies applied to the de novo assembly of a plant genome, Macadamia jansenii. We have generated sequencing data using Pacific Biosciences (Sequel I), Oxford Nanopore Technologies (PromethION), and BGI (single-tube Long Fragment Read) technologies for the same sample. Several assemblers were benchmarked in the assembly of Pacific Biosciences and Nanopore reads. Results obtained from combining long-read technologies or short-read and long-read technologies are also presented. The assemblies were compared for contiguity, base accuracy, and completeness, as well as sequencing costs and DNA material requirements. Conclusions The 3 long-read technologies produced highly contiguous and complete genome assemblies of M. jansenii. At the time of sequencing, the cost associated with each method was significantly different, but continuous improvements in technologies have resulted in greater accuracy, increased throughput, and reduced costs. We propose updating this comparison regularly with reports on significant iterations of the sequencing technologies.

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Section: Methodsmentioning

confidence: 99%

Comparison of long-read methods for sequencing and assembly of a plant genome

et al. 2020

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“…More detailed pipeline about scaffolding using Hi-C data is as described on protocol.io (dx.doi.org/10.17504/protocols.io.qradv2e, last accessed March 3, 2021). For the male genome, we used SUPERNOVA with 10X Genomics for initial assembly, then GAPCLOSER with short reads to fill gaps and TGS-GapCloser v1.0.0 ( Xu et al. 2020 ) with Nanopore reads to rescaffold using default parameters, and we finally used 3DDNA with Hi-C data to elevate the assembly to chromosome levels.…”

Section: Methodsmentioning

confidence: 99%

Reconstruction of the Origin of a Neo-Y Sex Chromosome and Its Evolution in the Spotted Knifejaw,Oplegnathus punctatus

Zhang²,

Fan³

et al. 2021

Molecular Biology and Evolution

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Sex chromosomes are a peculiar constituent of the genome because the evolutionary forces that fix the primary sex-determining gene cause genic degeneration and accumulation of junk DNA in the heterogametic partner. One of the most spectacular phenomena in sex chromosome evolution is the occurrence of neo-Y chromosomes, which lead to X1X2Y sex-determining systems. Such neo-sex chromosomes are critical for understanding the processes of sex chromosome evolution because they rejuvenate their total gene content. We assembled the male and female genomes at the chromosome level of the spotted knifejaw (Oplegnathus punctatus), which has a cytogenetically recognized neo-Y chromosome. The full assembly and annotation of all three sex chromosomes allowed us to reconstruct their evolutionary history. Contrary to other neo-Y chromosomes, the fusion to X2 is quite ancient, estimated at 48 Mya. Despite its old age and being even older in the X1 homologous region which carries a huge inversion that occurred as early as 55-48 Mya, genetic degeneration of the neo-Y appears to be only moderate. Transcriptomic analysis showed that sex chromosomes harbor 87 genes, which may serve important functions in the testis. The accumulation of such male-beneficial genes, a large inversion on the X1 homologous region and fusion to X2 appear to be the main drivers of neo-Y evolution in the spotted knifejaw. The availability of high-quality assemblies of the neo-Y and both X chromosomes make this fish an ideal model for a better understanding of the variability of sex determination mechanisms and of sex chromosome evolution.

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“…Long reads provide an effective and cost-efficient means to close gaps in fragmented assemblies, since these reads are often longer than genomic repeats, allowing one to bridge between neighboring contigs thus closing an assembly gap [7]. To close gaps in existing, more fragmented assemblies with long reads, several methods have been developed in the past, exemplified by PBJelly [8], FinisherSC [9], PacBio GenomicConsensus (PacBio GC; comprising the Arrow and Quiver methods; https://github.com/PacificBiosciences/GenomicConsensus), LR_gapcloser [10] and others [11][12][13]. These methods align a set of given long reads to an input assembly, determine which reads span assembly gaps and close these gaps with the new sequence.…”

Section: Introductionmentioning

confidence: 99%

DENTIST – using long reads for closing assembly gaps at high accuracy

Ludwig

Pippel

Myers

et al. 2021

Preprint

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Long sequencing reads allow increasing contiguity and completeness of fragmented, short-read based genome assemblies by closing assembly gaps, ideally at high accuracy. While several gap closing methods have been developed, these methods often close an assembly gap with sequence that does not accurately represent the true sequence. Here, we developed DENTIST, a sensitive, highly-accurate and automated pipeline method to close gaps in short read assemblies with long reads. DENTIST comprehensively determines repetitive assembly regions to identify reliable and unambiguous alignments of long reads to the right loci, integrates a consensus sequence computation step to obtain a high base accuracy for the inserted sequence, and validates the accuracy of closed gaps. Unlike previous benchmarks, we generated test assemblies that have gaps at the exact positions where real short-read assemblies have gaps. Generating such realistic benchmarks for Drosophila (134 Mb genome), Arabidopsis (119 Mb), hummingbird (1 Gb) and human (3 Gb) and using simulated or real PacBio reads, we show that DENTIST consistently achieves a substantially higher accuracy compared to previous methods, while having a similar sensitivity. As another distinguishing feature, DENTIST can accurately scaffold the given contigs with long reads in addition to closing gaps, extending its application range to contig-only assemblies. In summary, DENTIST provides an accurate approach to improve the contiguity and completeness of fragmented assemblies with long reads. DENTIST's source code including a Snakemake workflow and Docker container is available at https://github.com/a-ludi/dentist. All test assemblies as a resource for future benchmarking are at https://bds.mpi-cbg.de/hillerlab/DENTIST/.

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TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads

Cited by 244 publications

References 46 publications

Comparison of long-read methods for sequencing and assembly of a plant genome

Comparison of long-read methods for sequencing and assembly of a plant genome

Reconstruction of the Origin of a Neo-Y Sex Chromosome and Its Evolution in the Spotted Knifejaw,Oplegnathus punctatus

DENTIST – using long reads for closing assembly gaps at high accuracy

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