C
Chen-Shan Chin
Researcher at Pacific Biosciences
Publications - 83
Citations - 17070
Chen-Shan Chin is an academic researcher from Pacific Biosciences. The author has contributed to research in topics: Genome & Sequence assembly. The author has an hindex of 38, co-authored 77 publications receiving 13370 citations. Previous affiliations of Chen-Shan Chin include University of Washington & University of California, San Francisco.
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Journal ArticleDOI
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
Chen-Shan Chin,David Alexander,Patrick Marks,Aaron Klammer,James P Drake,Cheryl Heiner,Alicia Clum,Alex Copeland,John Huddleston,Evan E. Eichler,Stephen Turner,Jonas Korlach +11 more
TL;DR: This work presents a hierarchical genome-assembly process (HGAP) for high-quality de novo microbial genome assemblies using only a single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing.
Journal ArticleDOI
Phased diploid genome assembly with single-molecule real-time sequencing
Chen-Shan Chin,Paul Peluso,Fritz J. Sedlazeck,Maria Nattestad,Gregory T. Concepcion,Alicia Clum,Christopher Dunn,Ronan C. O'Malley,Rosa Figueroa-Balderas,Abraham Morales-Cruz,Grant R. Cramer,Massimo Delledonne,Chongyuan Luo,Joseph R. Ecker,Dario Cantu,David R. Rank,Michael C. Schatz,Michael C. Schatz +17 more
TL;DR: The open-source FALCON and FALcon-Unzip algorithms are introduced to assemble long-read sequencing data into highly accurate, contiguous, and correctly phased diploid genomes.
Journal ArticleDOI
Improved maize reference genome with single-molecule technologies
Yinping Jiao,Paul Peluso,Jinghua Shi,Tiffany Y. Liang,Michelle C. Stitzer,Bo Wang,Michael S. Campbell,Joshua C. Stein,Xuehong Wei,Chen-Shan Chin,Katherine E. Guill,Michael Regulski,Sunita Kumari,Andrew Olson,Jonathan I. Gent,Kevin L. Schneider,Thomas K. Wolfgruber,Michael R. May,Nathan M. Springer,Eric Antoniou,W. Richard McCombie,Gernot G. Presting,Michael D. McMullen,Jeffrey Ross-Ibarra,R. Kelly Dawe,Alex Hastie,David R. Rank,Doreen Ware,Doreen Ware +28 more
TL;DR: The assembly and annotation of a reference genome of maize is reported, using single-molecule real-time sequencing and high-resolution optical mapping to identify transposable element lineage expansions that are unique to maize.
Journal ArticleDOI
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
Konstantin Berlin,Sergey Koren,Chen-Shan Chin,James P Drake,Jane M. Landolin,Adam M. Phillippy +5 more
TL;DR: The MinHash Alignment Process (MHAP) is introduced for overlapping noisy, long reads using probabilistic, locality-sensitive hashing and can produce de novo near-complete eukaryotic assemblies that are 99.99% accurate when compared with available reference genomes.
Journal ArticleDOI
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.
Aaron M. Wenger,Paul Peluso,William J Rowell,Pi-Chuan Chang,Richard Hall,Gregory T. Concepcion,Jana Ebler,Arkarachai Fungtammasan,Alexander Kolesnikov,Nathan D. Olson,Armin Töpfer,Michael Alonge,Medhat Mahmoud,Yufeng Qian,Chen-Shan Chin,Adam M. Phillippy,Michael C. Schatz,Gene Myers,Mark A. DePristo,Jue Ruan,Tobias Marschall,Tobias Marschall,Fritz J. Sedlazeck,Justin M. Zook,Heng Li,Sergey Koren,Andrew Carroll,David R. Rank,Michael W. Hunkapiller +28 more
TL;DR: The optimization of circular consensus sequencing (CCS) is reported to improve the accuracy of single-molecule real-time (SMRT) sequencing (PacBio) and generate highly accurate (99.8%) long high-fidelity (HiFi) reads with an average length of 13.5 kilobases (kb).