Mario Caccamo, head of bioinformatics at The Genome Analysis Centre (TGAC) in the UK, integrates many different sequencing technologies to get the best of each for optimal genome assemblies, analysis, and annotation. He uses PacBio’s SMRT Sequencing due to its unique long reads for scaffolding and finishing genomes.
Mario Caccamo, head of bioinformatics at The Genome Analysis Centre (TGAC) in the UK, integrates many different sequencing technologies to get the best of each for optimal genome assemblies, analysis, and annotation. He uses PacBio’s SMRT Sequencing due to its unique long reads for scaffolding and finishing genomes.
Sergey Koren of the National Biodefense Analysis and Countermeasures Center (NBACC) discusses integrating the MinHash Alignment Process (MHAP) with Celera Assembler to enable reference-grade assemblies of model organisms, revealing novel heterochromatic sequences and filling low-complexity gap sequences in the GRCh38 human reference genome. Dr. Koren and his team have applied this method to assemble the San Clemente goat genome. Combining SMRT Sequencing and next-generation optical mapping from BioNano Genomics generates an assembly that is over 150-fold more contiguous than the latest Capra hircusgoat reference. In combination with Hi-C sequencing, the assembly surpasses reference assemblies de novo, with minimal manual intervention.…
Tim Smith, molecular geneticist at the USDA Agricutural Research Service (ARS) in Clay Center, Nebraska, and director of the U.S. Meat Animal Reseach Center Core Facilities, discusses the USDA’s efforts to improve the goat, swine, cattle, and sheep genomes through long read-based de novoassemblies scaffolded with a variety of approaches. Recent advances in long-read sequencing, combined with new technologies for scaffolding the resulting contigs, have made it possible to make a significant change in the quality of genome assemblies for a very small fraction of the price required to create the originals. Although a change of reference genomes incurs cost,…
Grant Cramer from the University of Nevada, Reno, and Dario Cantu from the Univeristy of Callifornia, Davis, discuss past challenges with sequencing Clone 8 of Cabernet Sauvignon (Vitis vinifera). An assembly of the genome was attempted with approximately 110x Illumina reads and 5x PacBio reads. The PacBio SMRT Sequencing read made major improvements in the assembly compared with the results of Illumina reads only. However, the assembly results were still unsatisfactory, so an additional 100-fold SMRT Sequencing coverage had been generated. An update on the current sequencing results and status of the assembly are presented.
Karyn Meltz Steinberg presents the first high quality African reference genome assembly of the Yoruban individual, NA19240, produced from SMRT Sequencing data. She said PacBio sequencing offers significant improvement over short-read sequence data for high-quality assemblies.
Rebecca Johnson, director of the Australian Museum Research Institute presents finding from de novo sequencing of the koala genome. Using PacBio sequencing the Koala Genome Consortium obtained an assembly with an N50 of 11.5 Mbp and have undertaken functional genomic analysis highlighting the unique genes associated with lactation and immune function of koalas. Johnson goes on to describe efforts to obtain a chromosome level assembly and current work using ‘super scaffolding’ to compare shared synteny across diverse lineages to generate chromosome scaffold maps.
At PAG 2017, Rockefeller University’s Erich Jarvis offered an in-depth comparison of methods for generating highly contiguous genome assemblies, using hummingbird as the basis to evaluate a number of sequencing and scaffolding technologies. Analyses include gene content, error rate, chromosome metrics, and more. Plus: a long-read look at four genes associated with vocal learning.
In this AGBT 2017 poster, Ulf Gyllensten from Uppsala University presents two local reference genomes generated with PacBio and Bionano Genomics data. These assemblies include structural variation and repetitive regions that have been missed with previous short-read efforts, including some new genes not annotated in the human reference genome.
In a poster presented at AGBT 2017, Fritz Sedlazeck from Johns Hopkins University describes the comparison of genome assemblies produced using long-read PacBio sequencing and short-read sequencing with 10x Genomics scaffolding. An alignment reveals regions missed by the short-read assembly, including repeats, exons, and even whole genes.
At AGBT 2017, the Broad Institute’s Daniel Neafsey reported a large collaborative effort to sequence the mosquito that carries Zika virus. The team is using long-read PacBio sequencing to produce a high-quality genome assembly, which Neafsey expects will replace the 10-year-old Sanger assembly for Aedes aegypti. The new assembly reduces the number of contigs by at least 10-fold, boosts the contig N50 to nearly 2 Mb, and features more complete gene content.
In this PacBio User Group Meeting presentation, Tina Graves-Lindsay of the McDonnell Genome Institute and the Genome Reference Consortium speaks about the importance of phasing human reference genomes. Her team is now working on its fifteenth human genome assembly — part of a major effort to improve genomic representation of ethnic diversity — with a pipeline that generates 60-fold PacBio coverage for a de novo assembly, followed by scaffolding with other technologies. They are also using FALCON-Unzip to separate haplotypes, leading to reference-grade diploid assemblies. This approach has already helped resolve errors seen in other genomes and even the gold-standard…
To make improvements to crops like corn, soybeans, and canola, scientists at Corteva are building a compendium of crop genomics resources to provide actionable sequence info for genetic discovery, gene-editing, and seed product development. Hear how Kevin Fengler, Comparative Genomics Lead of Data Science and Bioinformatics at Corteva, is using PacBio sequences to build visualization tools and genome assembly pipelines as a contribution to this effort.
In this webinar, Jonas Korlach, Chief Scientific Officer, PacBio provides an overview of the features and the advantages of the new Sequel II System. Kiran Garimella, Senior Computational Scientist, Broad Institute of MIT and Harvard University, describes his work sequencing humans with HiFi reads enabling discovery of structural variants undetectable in short reads. Luke Tallon, Scientific Director, Genomics Resource Center, Institute for Genome Sciences, University of Maryland School of Medicine, covers the GRC’s work on bacterial multiplexing, 16S microbiome profiling, and shotgun metagenomics. Finally, Shane McCarthy, Senior Research Associate, University of Cambridge, focuses on the scaling and affordability of high-quality…
In a push to develop insect-based food sources for people, Brenda Oppert from the USDA has been sequencing bug genomes with PacBio technology. Long reads are essential because of the highly repetitive sequences and large genomes. On the Sequel II System, a single SMRT Cell is sufficient to generate 350-fold coverage and produce a high-quality assembly for some of the insects she’s studying.