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Monday, October 17, 2016

New FALCON Tools Enable Diploid Assemblies from SMRT Sequencing Data

In a Nature Methods paper released today, scientists describe the new bioinformatics tools to produce diploid genome assemblies from SMRT Sequencing reads. FALCON (Fast ALignment and CONsensus for assembly) and FALCON-Unzip were developed by PacBio scientists in collaboration with researchers at Johns Hopkins University, Cold Spring Harbor Laboratory, the Joint Genome Institute, and other institutions. “Phased diploid genome assembly with single-molecule real-time sequencing” comes from lead authors Chen-Shan Chin and Paul Peluso, senior author Michael Schatz, and collaborators. In the publication, the team details how FALCON and FALCON-Unzip work and presents data from several validation studies of organisms including Arabidopsis,…

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Friday, October 2, 2015

Toward Platinum Genomes: PacBio Releases a New, Higher-Quality CHM1 Assembly to NCBI

As part of our effort to support the National Institutes of Health and the Genome Reference Consortium (GRC) in creating platinum genomes for the research community and improving the reference genome, in 2014 we generated 54X SMRT® Sequencing coverage of the CHM1 cell line, derived from a human haploid hydatidiform mole, using our P5-C3 chemistry, and made it publicly available through the SRA database at NCBI. The CHM1 dataset was quickly taken up by researchers eager to use long, unbiased reads to identify regions of the genome prone to structural variation and to fill in sequence gaps in the GRC-maintained…

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Friday, June 27, 2014

At SFAF 2014, Great Science and High-Quality Genomes

It’s been a busy start to the summer, but we’re still basking in the top-notch presentations and posters from the Sequencing, Finishing, and Analysis in the Future meeting last month. Hosted by Los Alamos National Laboratory in Santa Fe, this has become a premier event for scientists working on sequencing protocols, analysis, and assembly methods. Many speakers presented data including reads from Single Molecule, Real-Time (SMRT®) Sequencing. Jeff Rogers from Baylor College of Medicine used long PacBio® reads with the PBJelly algorithm to fill gaps in many mammalian genomes, including sheep, rat, baboon, sooty mangabey, and mouse lemur. Tina Graves-Lindsay…

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Wednesday, February 12, 2014

Data Release: ~54x Long-Read Coverage for PacBio-only De Novo Human Genome Assembly

We are pleased to make publicly available a new shotgun sequence dataset of long PacBio® reads from a human DNA sample. We previously released sequence data using Single Molecule, Real-Time (SMRT®) Sequencing of ~10x coverage of this sample, sufficient for reference-based detection of structural variation. Today we expand on that release with additional data that increases the total sequencing coverage to ~54x.  This long-read data has enabled the generation of the first de novo human genome assembly from PacBio-only sequence reads. Download the 54x long-read coverage dataset. The dataset was generated from sequencing a well-studied human cell line (CHM1htert), which…

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