Explanipedia

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing Open

Sergey Koren, Zhigui Bao, Andrea Guarracino, Shujun Ou, Sara Goodwin , et al. · 2024

The combination of ultra-long (UL) Oxford Nanopore Technologies (ONT) sequencing reads with long, accurate Pacific Bioscience (PacBio) High Fidelity (HiFi) reads has enabled the completion of a human genome and spurred similar efforts to c…

Highly accurate assembly polishing with DeepPolisher Open

Mira Mastoras, Mobin Asri, Lucas Brambrink, Prajna Hebbar, Alexey Kolesnikov , et al. · 2024

Accurate genome assemblies are essential for biological research, but even the highest quality assemblies retain errors caused by the technologies used to construct them. Base-level errors are typically fixed with an additional polishing s…

Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph Open

Haoyu Cheng, Mobin Asri, Julian Lucas, Sergey Koren, Heng Li · 2024

Phased nanopore assembly with Shasta and modular graph phasing with GFAse Open

Ryan Lorig-Roach, Melissa Meredith, Jean Monlong, Miten Jain, Hugh E. Olsen , et al. · 2024

Reference-free genome phasing is vital for understanding allele inheritance and the impact of single-molecule DNA variation on phenotypes. To achieve thorough phasing across homozygous or repetitive regions of the genome, long-read sequenc…

The variation and evolution of complete human centromeres Open

Glennis A. Logsdon, Allison N. Rozanski, Fedor Ryabov, Tamara Potapova, В. А. Шепелев , et al. · 2024

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing Open

Sergey Koren, Zhigui Bao, Andrea Guarracino, Shujun Ou, Sara Goodwin , et al. · 2024

The combination of ultra-long Oxford Nanopore (ONT) sequencing reads with long, accurate PacBio HiFi reads has enabled the completion of a human genome and spurred similar efforts to complete the genomes of many other species. However, thi…

The complete sequence of a human Y chromosome Open

Arang Rhie, Sergey Nurk, Monika Čechová, Savannah J. Hoyt, Dylan J. Taylor , et al. · 2023

Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome Open

HoJoon Lee, Stephanie Greer, Dmitri S. Pavlichin, Bo Zhou, Alexander E. Urban , et al. · 2023

The human pangenome, a new reference sequence, addresses many limitations of the current GRCh38 reference. The first release is based on 94 high-quality haploid assemblies from individuals with diverse backgrounds. We employed a k-mer inde…

HPRC Y1 assemblies (HiFi + UL) evaluated in the hifiasm (UL) paper Open

Haoyu Cheng, Mobin Asri, Julian Lucas, Sergey Koren, Heng Li · 2023

This repository contains all HPRC Y1 assemblies evaluated in the paper titled: Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph.

The variation and evolution of complete human centromeres Open

Glennis A. Logsdon, Allison N. Rozanski, Fedor Ryabov, Tamara Potapova, В. А. Шепелев , et al. · 2023

We completely sequenced and assembled all centromeres from a second human genome and used two reference sets to benchmark genetic, epigenetic, and evolutionary variation within centromeres from a diversity panel of humans and apes. We find…

Plant assemblies evaluated in the hifiasm (UL) paper Open

Haoyu Cheng, Mobin Asri, Julian Lucas, Benedict Paten, Heng Li · 2023

This repository contains all plant assemblies evaluated in the paper titled: Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph.

Pangenome graph construction from genome alignments with Minigraph-Cactus Open

Glenn Hickey, Jean Monlong, Jana Ebler, Adam M. Novak, Jordan M. Eizenga , et al. · 2023

A draft human pangenome reference Open

Wen‐Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness , et al. · 2023

Increased mutation and gene conversion within human segmental duplications Open

Mitchell R. Vollger, Philip C. Dishuck, William T. Harvey, William S. DeWitt, Xavi Guitart , et al. · 2023

Recombination between heterologous human acrocentric chromosomes Open

Andrea Guarracino, Silvia Buonaiuto, Leonardo Gomes de Lima, Tamara Potapova, Arang Rhie , et al. · 2023

The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats and extended segmental duplications 1,2 . Although the resolution of these regions in the fir…

Preliminary assemblies of the three-generational pedigree of African-American ancestry Open

Monika Čechová, Sergey Koren, Julian Lucas, Rebecca Serra Mari, Mobin Asri , et al. · 2023

Monika Cechova¹, Sergey Koren², Julian K. Lucas¹, Rebecca Serra Mari³, Mobin Asri¹, David Porubsky⁴, Jordan M. Eizenga¹, Brandy McNulty¹, Andrey Bzikad…

Preliminary assemblies of the three-generational pedigree of African-American ancestry Open

Monika Čechová, Sergey Koren, Julian Lucas, Rebecca Serra Mari, Mobin Asri , et al. · 2023

Monika Cechova¹, Sergey Koren², Julian K. Lucas¹, Rebecca Serra Mari³, Mobin Asri¹, David Porubsky⁴, Jordan M. Eizenga¹, Brandy McNulty¹, Andrey Bzikad…

Phased nanopore assembly with Shasta and modular graph phasing with GFAse Open

Ryan Lorig-Roach, Melissa Meredith, Jean Monlong, Miten Jain, Hugh E. Olsen , et al. · 2023

As a step towards simplifying and reducing the cost of haplotype resolved de novo assembly, we describe new methods for accurately phasing nanopore data with the Shasta genome assembler and a modular tool for extending phasing to the chrom…

Co-Linear Chaining on Pangenome Graphs Open

Haoyu Cheng, Mobin Asri, Julian Lucas, Sergey Koren, Heng Li · 2023

Pangenome reference graphs are useful in genomics because they compactly represent the genetic diversity within a species, a capability that linear references lack. However, efficiently aligning sequences to these graphs with complex topol…

The complete sequence of a human Y chromosome Open

Arang Rhie, Sergey Nurk, Monika Čechová, Savannah J. Hoyt, Dylan J. Taylor , et al. · 2022

The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure including long palindromes, tandem repeats, and segmental duplications 1–3 . As a result, more than half of the Y chromo…

Semi-automated assembly of high-quality diploid human reference genomes Open

Erich D. Jarvis, Giulio Formenti, Arang Rhie, Andrea Guarracino, Chentao Yang , et al. · 2022

The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society 1,2 . However, it still has many gaps and errors, and does not represent a biological genome a…

A Draft Human Pangenome Reference Open

Wen‐Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness , et al. · 2022

The Human Pangenome Reference Consortium (HPRC) presents a first draft human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals. These assemblies cover more than 99% o…

Increased mutation rate and interlocus gene conversion within human segmental duplications Open

Mitchell R. Vollger, William S. DeWitt, Philip C. Dishuck, William T. Harvey, Xavi Guitart , et al. · 2022

Single-nucleotide variants (SNVs) within segmental duplications (SDs) have not been systematically assessed because of the difficulty in mapping short-read sequence data to virtually identical repetitive sequences. Using 102 phased human h…

The Human Pangenome Project: a global resource to map genomic diversity Open

Ting Wang, Lucinda Antonacci-Fulton, Kerstin Howe, Heather A. Lawson, Julian Lucas , et al. · 2022

Complete genomic and epigenetic maps of human centromeres Open

Nicolas Altemose, Glennis A. Logsdon, Andrey V. Bzikadze, Pragya Sidhwani, Sasha A. Langley , et al. · 2022

Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, and functions, which include facilitating proper chromosome segre…

Automated assembly of high-quality diploid human reference genomes Open

Erich D. Jarvis, Giulio Formenti, Arang Rhie, Andrea Guarracino, Chentao Yang , et al. · 2022

The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has greatly benefited society 1, 2 . However, it still has many gaps and errors, and does not represent a biological …

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space Open

Michael C. Schatz, Anthony Philippakis, Enis Afgan, Eric Banks, Vincent J. Carey , et al. · 2022

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