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Author Archives: Alex
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
Comments Off on Sage Sizing Platforms Recommended for 10x Genomics Libraries
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
Long-read sequencing and de novo assembly of a Chinese genome
June 2016 Authors: Lingling Shi, Yunfei Guo, Chengliang Dong, John Huddleston, Hui Yang, et al. Info: Scientists in China and the US analyzed the DNA and RNA of a Chinese individual, using PacBio sequencing and BioNano Genomics maps to produce … more »
Posted in Citation
Tagged BluePippin, PacBio
Comments Off on Long-read sequencing and de novo assembly of a Chinese genome
New GIAB Publication Characterizes Seven Genomes with 12 Technologies
The Genome in a Bottle Consortium is on a roll — and if you haven’t checked out the latest paper in Scientific Data, you’re missing out. “Extensive sequencing of seven human genomes to characterize benchmark reference materials” comes from lead … more »
Posted in Blog
Tagged BluePippin
Comments Off on New GIAB Publication Characterizes Seven Genomes with 12 Technologies