Citations

Mapping and phasing of structural variation in patient genomes using nanopore sequencing

November 2017

Authors:
Mircea Cretu Stancu, Markus van Roosmalen, Ivo Renkens, Marleen Nieboer, et al.

Info:
Scientists used the Oxford MinION nanopore sequencer with a novel pipeline, NanoSV, to detect structural variants from the genomes of two patients. They found that long reads are better than short reads at detecting events such as de novo chromothripsis rearrangements. The team used PippinHT for size-selecting libraries prior to sequencing.

Citation:
Nature Communications 8: 1326 (2017)
doi: 10.1038/s41467-017-01343-4

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Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts

November 2017

Authors:
Bing Cheng, Agnelo Furtado, Robert Henry

Info:
In this study, researchers generated the transcriptome of the tetraploid Arabica coffee bean, focusing on caffeine and sucrose genes for in-depth analysis. They used the PacBio Iso-Seq method with BluePippin selection for four library size ranges.

Citation:
GigaScience, Volume 6, Issue 11, Pages 1–13
doi: 10.1093/gigascience/gix086

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De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing

October 2017

Authors:
Maximilian Schmidt, Alxander Vogel, Alisandra Denton, Benjamin Istace, et al.

Info:
Scientists used Oxford Nanopore technology to sequence Solanum pennellii, a wild species of tomato. They generated a median read length of nearly 12 Kb and produced an assembly with a contig N50 of 2.5 Mb. The high error rate was reduced by polishing with Illumina reads. The team enriched for long reads by using BluePippin to remove smaller fragments prior to sequencing.

Citation:
The Plant Cell
doi: 10.1105/tpc.17.00521

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A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value

October 2017

Authors:
Changsong Zou, Aojun Chen, Lihong Xiao, Heike Muller, et al.

Info:
Scientists deployed several sequencing platforms to characterize the genome of Chenopodium quinoa, an important and highly nutritious cereal crop. They analyzed the assembly to better understand the plant’s remarkable stress tolerance and its genomic evolution. SageELF was used to prepare DNA fractions for PCR-free library construction in an Illumina workflow.

Citation:
Cell Research (2017) 27, 1327–1340 (2017)
doi:10.1038/cr.2017.124

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Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify

October 2017

Authors:
Malgorzata Komor, Thang Pham, Annemieke Hiemstra, Sander Piersma, et al.

Info:
In this paper, scientists from the Netherlands Cancer Institute, VU University Medical Center, and other institutions describe results from a new pipeline to detect differentially expressed protein isoforms. The method uses RNA sequencing and tandem mass spectrometry. In validation studies, the team used SageELF to separate library fractions into several size bins.

Citation:
Molecular & Cellular Proteomics 16,1850-1863
doi:10.1074/mcp.TIR117.000056

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