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 used PacBio sequencing to examine alternative splicing in sorghum. Their transcriptome analysis led to the discovery of thousands of novel splicing events, isoforms, and genes. BluePippin was used to size-select libraries prior to sequencing.
Citation:
Nature Communications
doi:10.1038/ncomms11706
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 in more accurate SNP detection even for rare variants. Pippin Prep was used for tight sizing of sequencing libraries prior to paired-end Illumina sequencing.
Citation
BMC Genomics 201617:464
DOI: 10.1186/s12864-016-2669-3
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. The team used PippinHT for automated DNA size selection prior to sequencing with Ion Torrent.
Citation:
Nature Methods
doi:10.1038/nmeth.3893
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 a high-quality assembly. They report a significant amount of new sequence data and novel gene content, including elements that appear to be specific to the Asian population. The team used BluePippin for size selection prior to genome and transcriptome sequencing with PacBio.
Citation:
Nature Communications
doi:10.1038/ncomms12065
Extensive sequencing of seven human genomes to characterize benchmark reference materials
June 2016
Authors:
Justin M. Zook, David Catoe, Jennifer McDaniel, Lindsay Vang, et al.
Info:
The Genome in a Bottle Consortium used 12 different DNA analysis technologies to generate deep data sets on seven genomes, five of which will become reference materials for the community. BluePippin was used with various platforms, including PacBio and SOLiD.
Citation:
Scientific Data 2016; 3: 160025.
DOI 10.1038/sdata.2016.25