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Monthly Archives: July 2016
Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing
June 2016 Authors: Shruthi Sridhar Vembar, Matthew Seetin, Christine Lambert, Maria Nattestad, Michael C. Schatz, Primo Baybayan, Artur Scherf, and Melissa Laird Smith Info: Scientists in France and the US used PacBio sequencing to characterize the AT-rich genome of this … more »
Posted in Citation
Tagged BluePippin, High Pass, Pippin Pulse
Comments Off on Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing
A survey of the sorghum transcriptome using single-molecule long reads
June 2016 Authors: Salah E. Abdel-Ghany, Michael Hamilton, Jennifer L. Jacobi, Peter Ngam, Nicholas Devitt, Faye Schilkey, Asa Ben-Hur & Anireddy S. N. Reddy Info: In this publication, scientists from Colorado State University and the National Center for Genome Resources … more »
Posted in Citation
Tagged BluePippin, isoseq, PacBio, RNAseq, transcriptome
Comments Off on A survey of the sorghum transcriptome using single-molecule long reads
PELE-seq Increases SNP Calling Accuracy by Reducing Sequencing Errors
Scientists at the University of Oregon have published a new method to detect PCR and sequencing errors that should help other researchers track rare SNPs with greater accuracy. PELE-seq, which gets our vote for best new protocol name, can be … more »
Posted in Blog
Tagged ddRADseq, genotyping, HiSeq, Illumina, Methods, Pippin Prep
Comments Off on PELE-seq Increases SNP Calling Accuracy by Reducing Sequencing Errors
High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)
June 2016 Authors: Jessica L. Preston, Ariel E. Royall, Melissa A. Randel, Kristin L. Sikkink, Patrick C. Phillips, and Eric A. Johnson Info: Scientists at the University of Oregon developed a new protocol to reduce sequencing and PCR errors, resulting … more »
Posted in Citation
Comments Off on High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)
Low-Coverage Sequencing No Challenge for Structural Variant Detection
Is it really possible to detect somatic structural variants accurately from a single sequencing read? A new protocol from scientists at the Albert Einstein College of Medicine in New York and Voronezh State University in Russia was designed to do … more »
Posted in Blog
Tagged Ion Torrent, PippinHT
Comments Off on Low-Coverage Sequencing No Challenge for Structural Variant Detection
Quantitative detection of low-abundance somatic structural variants in normal cells by high-throughput sequencing
June 2016 Authors: Wilber Quispe-Tintaya, Tatyana Gorbacheva, Moonsook Lee, Sergei Makhortov, Vasily N Popov, Jan Vijg & Alexander Y Maslov Info: Scientists report Structural Variant Search, a new method for detecting rare somatic structural variants even with low-coverage sequencing data. … more »
Sage Sizing Platforms Recommended for 10x Genomics Libraries
We’re pleased to report that 10x Genomics has released a new sample prep protocol for its Chromium platform that includes the BluePippin and PippinHT size selection platforms from Sage Science. 10x Genomics has gotten a lot of attention in recent … more »
Posted in Blog
Tagged 10X, BluePippin, PippinHT
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Double Pippin for Optimized RAD-seq
Scientists in China and the UK recently published an open-access optimized protocol for RAD-seq in the Theoretical and Applied Genetics journal. The method is targeted at large studies of plants and enables users to specify sequence coverage parameters. From lead … more »
Podcast: Kari Stefansson on 20 Years of Human Genomics
Mendelspod has turned out another terrific podcast, this one with Kari Stefansson, and we’re proud to have sponsored the thought-provoking discussion. As most people in the field know, Stefansson earned his fame as founder of DeCode Genetics, which has spent … more »
Scientists Use Multiple Technologies to Produce High-Quality Chinese Genome Assembly
A newly reported genome assembly of a Chinese individual, generated by scientists in China and the US, used long-read PacBio sequencing, short-read Illumina data, and BioNano Genomics physical maps to achieve remarkably high accuracy and contiguity. Along the way, the … more »
Posted in Blog
Tagged BluePippin, PacBio
Comments Off on Scientists Use Multiple Technologies to Produce High-Quality Chinese Genome Assembly