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Wednesday, February 21, 2018

Hummingbird Study Uses Iso-Seq Method to Hunt for Metabolic Function

[caption id="attachment_14026" align="alignright" width="288"] Photo of ruby-throated hummingbird by Michelle Lynn Reynolds[/caption] UPDATED February 21, 2018 Congratulations to Winston Timp's team on the publication of their Iso-Seq analysis of hummingbird! The paper is now available at GigaScience. ORIGINAL POST April 4, 2017 A new preprint offers an enticing look at transcriptome results from analysis of a hummingbird using SMRT Sequencing. In this study, scientists found new clues to explain unique attributes of the bird’s metabolism. The work was made possible through full-length isoform sequencing, which allowed deep, assembly-free analysis even though no reference genome was available. “Single molecule, full-length transcript…

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Monday, June 12, 2017

Scientists Use SMRT Sequencing to Reveal Unexpected Adhesin Repertoire in Candida

[caption id="attachment_17356" align="alignright" width="300"] Candida glabrata[/caption] In a preprint available from bioRxiv, scientists from the University of Lausanne and Swiss Institute of Bioinformatics present the first SMRT Sequencing results from isolates of the fungal pathogen Candida glabrata. “Comparative Genomics Of Two Sequential Candida glabrata Clinical Isolates” comes from Luis Andre Vale-Silva, Emmanuel Beaudoing, Van Du T. Tran, and Dominique Sanglard. The study involved two C. glabrata samples collected at different times from an HIV-positive patient diagnosed with oropharyngeal candidiasis. Scientists initially turned to short-read sequencing to analyze the genomes, which were of particular interest because C. glabrata is known to rapidly develop resistance to antifungal therapies. However, because…

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Thursday, April 13, 2017

New QC Pipeline for Iso-Seq Data Increases Confidence in Transcript Results

A preprint from scientists at the University of Florida, Centro de Investigaciones Principe Felipe, and other institutes describes a new analysis tool to help boost quality of transcriptome studies. “SQANTI: extensive characterization of long read transcript sequences for quality control in full-length transcriptome identification and quantification” comes from lead author Manuel Tardaguila, senior author Ana Conesa, and collaborators. The automated pipeline for Structural and Quality Annotation of Novel Transcript Isoforms (SQANTI) was developed as a quality-assessment tool for transcripts discovered with SMRT Sequencing. SQANTI “calculates up to 35 different descriptors of transcript quality and creates a wide range of summary graphs to…

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