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How to Import data for libraries with index tags into BaseSpace

In this blog we describe how to import lists of sample data with defined index tags into BaseSpace, and provide templates for TruSeqLT and TruSeqHT libraries. We have found this saves a lot of time and eliminates errors associated with manual entry. The Illumina NextSeq500 sequencer requires all users to complete sample data entry on […]

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The dark arts of Ion Torrent Sequencing

All technologies, have their advantages and disadvantages, and next generation sequencing (NGS) is no different. For the time being, the current dominant forces in NGS are Illumina, which is based upon detecting a flash of light as fluorescent nucleotides are incorporated, or Ion Torrent, where nucleotide incorporation is detected in the form of a change […]

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1st Viral Bioinformatics and Genomics Training Course

The first Viral Bioinformatics and Genomics training course held at the University of Glasgow was completed successfully by 14 delegates (nine external and five internal) on 10-14 August 2015. The course took place in the McCall Building computer cluster, and the adjacent Lomond and Dumgoyne Rooms were used for refreshments and lunch. Instructors: Joseph Hughes […]

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A simple method to distinguish low frequency variants from Illumina sequence errors

RNA viruses have high mutation rates and exist within their hosts as large, complex and heterogeneous populations, comprising a spectrum of related but non-identical genome sequences. Next generation sequencing has revolutionised the study of viral populations by enabling the ultra deep sequencing of their genomes, and the subsequent identification of the full spectrum of variants […]

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Illumina adapter and primer sequences

Illumina Adapter and Primer Sequences Illumina libraries are normally constructed by ligating adapters to short fragments (100 – 1000bp) of DNA. The exception to this is if Nextera is used (see end of this post) or where PCR amplicons have been constructed that already incorporate the P5/P7 ends that bind to the flowcell. Illumina Paired […]

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Calculating dNdS for NGS datasets

vNvS Our upcoming tool vNvS calculates the dN/dS ratio at each site, codon and also for the sample as a whole, here is an explanation of the theory behind it. vNvS is currently in development – for more information email Richard.Orton@glasgow.ac.uk dN/dS dN/dS is the ratio of the number of nonsynonymous substitutions per non-synonymous site (pN) […]

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