Human Genome Assembly in 100 Minutes

Chin, Chen-Shan; Khalak, Asif

doi:10.1101/705616

Cited by 101 publications

(114 citation statements)

References 29 publications

Supporting

Mentioning

113

Contrasting

Order By: Relevance

“…We first evaluated HiCanu on a 24 kbp HiFi library from a Drosophila melanogaster F1 hybrid (ISO1×A4) (Data Availability). To match typical coverage, the HiFi dataset was downsampled to 40× and assembled with the HiFi-specific tools, HiCanu and Peregrine (Chin and Khalak 2019), as well as the conventional long-read assembler, Canu. Canu was chosen as it was previously shown to achieve the highest assembly continuity and superior repeat resolution among other popular long-read assemblers on HiFi data (Wenger et al 2019).…”

Section: Drosophila Genome Assemblymentioning

confidence: 99%

“…Many of these so-called "challenge" BACs were deliberately selected from genomic regions which pose significant assembly challenges (i.e. regions with segmental duplications), making them useful for assembly benchmarking (Chin and Khalak 2019;Shafin et al 2019;Miga et al 2019;Vollger et al 2020). Table 3 summarizes how well the challenge BACs are captured by different assemblies.…”

Section: Human Genome Assembliesmentioning

confidence: 99%

“…However, these early assemblies were limited to resolving repeats with greater than 1% sequence divergence, due to limitations of existing tools (Wenger et al 2019). The recently developed Peregrine assembler (Chin and Khalak 2019) greatly reduced assembly runtime and improved consensus accuracy, removing the need for post-processing, but did not address the issue of suboptimal repeat resolution or allele separation. Other recent work combined HiFi sequencing with complementary data types, such as parental information (Wenger et al 2019), Hi-C , and Strand-seq ) to obtain chromosome-scale, haplotype-resolved assemblies.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

Nurk

Walenz

Rhie

et al. 2020

Preprint

140

227

View full text Add to dashboard Cite

Complete and accurate genome assemblies form the basis of most downstream genomic analyses and are of critical importance. Recent genome assembly projects have relied on a combination of noisy long-read sequencing and accurate short-read sequencing, with the former offering greater assembly continuity and the latter providing higher consensus accuracy. The recently introduced PacBio HiFi sequencing technology bridges this divide by delivering long reads (>10 kbp) with high per-base accuracy (>99.9%). Here we present HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. We benchmark HiCanu with a focus on the recovery of haplotype diversity, major histocompatibility complex (MHC) variants, satellite DNAs, and segmental duplications. For diploid human genomes sequenced to 30× HiFi coverage, HiCanu achieved superior accuracy and allele recovery compared to the current state of the art. On the effectively haploid CHM13 human cell line, HiCanu achieved an NG50 contig size of 77 Mbp with a per-base consensus accuracy of 99.999% (QV50), surpassing recent assemblies of high-coverage, ultra-long Oxford Nanopore reads in terms of both accuracy and continuity. This HiCanu assembly correctly resolves 337 out of 341 validation BACs sampled from known segmental duplications and provides the first preliminary assemblies of 9 complete human centromeric regions. Although gaps and errors still remain within the most challenging regions of the genome, these results represent a significant advance towards the complete assembly of human genomes.Availability: HiCanu is implemented within the Canu assembly framework and is available from https://github.com/marbl/canu. This required 7 CPU h and 29 GB of memory for D. melanogaster, 32 CPU h and 347 GB of memory for CHM13 10 kbp library, 58 CPU h and 449 GB of memory for CHM13 20 kbp library, 55 CPU h and 407 GB for HG0002, and 63 CPU h and 477 GB for HG00733. Commands for β-defensin validation:MUmmer 3.23 was used to identify repeats with the command: nucmer --maxmatch --nosimplify delta-filter -i 98 -l 10000

show abstract

Section: Drosophila Genome Assemblymentioning

confidence: 99%

Section: Human Genome Assembliesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

Nurk

Walenz

Rhie

et al. 2020

Preprint

140

227

View full text Add to dashboard Cite

show abstract

“…It is possible that some MHC reads from HG002 are missed if they come from parts in the MHC region where HG002 is very different from the primary GRCh37 MHC region. In order to catch all possible reads that indeed belong to the MHC region of HG002, we also generated a de novo assembly of the HG002 MHC region using the Peregrine Assembler 22 and extracted reads that map to the de novo assembled contigs as unphased reads.…”

Section: Recruiting Wgs Reads For the Mhc Region Of Hg002mentioning

confidence: 99%

A Diploid Assembly-based Benchmark for Variants in the Major Histocompatibility Complex

Chin

Wagner

Zeng

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

We develop the first human benchmark derived from a diploid assembly for the openly-consented Genome in a Bottle/Personal Genome Project Ashkenazi son (HG002). As a proof-of-principle, we focus on a medically important, highly variable, 5 million base-pair region -the Major Histocompatibility Complex (MHC). Most human genomes are characterized by aligning individual reads to the reference genome, but accurate long reads and linked reads now enable us to construct base-level accurate, phased de novo assemblies from the reads. We assemble a single haplotig (haplotype-specific contig) for each haplotype, and align reads back to each assembled haplotig to identify two regions of lower confidence. We align the haplotigs to the reference, call phased small and structural variants, and define the first small variant benchmark for the MHC, covering 21496 small variants in 4.58 million base-pairs (92 % of the MHC). The assembly-based benchmark is 99.95 % concordant with a draft mapping-based benchmark from the same long and linked reads within both benchmark regions, but covers 50 % more variants outside the mapping-based benchmark regions. The haplotigs and variant calls are completely concordant with phased clinical HLA types for HG002. This benchmark reliably identifies false positives and false negatives from mapping-based callsets, and enables performance assessment in regions with much denser, complex variation than regions covered by previous benchmarks. These methods demonstrate a path towards future diploid assembly-based benchmarks for other complex regions of the genome.

show abstract

“…These results are comparable with the previous study 3 that used family trio information to haplotag 79.2% of HiFi PacBio reads. We next assembled haplotype-specific reads into completely phased de novo assemblies using one of the most popular assemblers, Canu 26 , and the recently described fast assembler for HiFi data, Peregrine 27 . While Peregrine generated more contiguous genome assemblies (N50 contig: H1: 28 Mbp, H2: 29.1 Mbp) compared to Canu (H1: 9.9 Mbp, H2: 10.7 Mbp), we noted more misassemblies, especially chimeric contigs, near the end of contigs ( Supplementary Table 1).…”

mentioning

confidence: 99%

A fully phased accurate assembly of an individual human genome

Porubský

Ebert

Audano

et al. 2019

Preprint

View full text Add to dashboard Cite

Figure 1: Conceptual overview of the complete genome assembly pipeline. a) In a single Strand-seq library only the template DNA strand (solid line) is sequenced for each parental homologous chromosome. b) Template strands of each homologue in a given diploid cell are randomly inherited by daughter cells ('+' positive strand, teal -Crick and '-' negative strand, orange -Watson), resulting in three possible template-strand states for homologous chromosomes (height of bars plotted along each chromosome represents the number of '+' and '-' reads mapped in each genomic bin): WC -one Crick and one Watson strand represented for given homologues; WW -only Watson template strands represented; or CC -only Crick template strands represented. c) Unassigned contigs follow the same pattern of template-strand-state inheritance based on the homologue they belong to. d) Contig order can be inferred based on low frequency changes in a templatestrand state resulting from sister chromatid exchange events (SCEs) in the parental cell: Contigs that are closer to each other tend to share the same template-strand state more often than more distant contigs. e) Regions with WC strand-state are haplotype informative and can be assembled into continuous haplotypes. f) Haplotypes can then be used to split long reads into their respective homologues. g) Generation of long-read (HiFi/CLR) based assemblies: i) Producing collapsed assemblies; ii) Assigning contigs to clusters using Strand-seq (StrandS); iii) Phasing clustered assemblies using the combination of Strand-seq and long PacBio reads; iv) Partitioning and reassembling of haplotype-specific PacBio reads and polishing of the final diploid assemblies.

show abstract

Human Genome Assembly in 100 Minutes

Cited by 101 publications

References 29 publications

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

A Diploid Assembly-based Benchmark for Variants in the Major Histocompatibility Complex

A fully phased accurate assembly of an individual human genome

Contact Info

Product

Resources

About