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6th Annual training course on Viral Bioinformatics and Genomics (21 – 25 August 2023)

April 13, 2023
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The MRC-University of Glasgow Centre for Virus Research (CVR) has been running a successful training course on Viral Bioinformatics and Genomics annually since 2015 and applications are now open for the 2023 course. This will be a 5-day course, which will consist of a series of lectures and practical exercises that directly address bioinformatic challenges […]

September 12, 2018
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From 20-24th Aug, we have held our 4th Viral Bioinformatics and Genomics training course at the Garscube campus of the University of Glasgow. In this year, our course had 16 participants attending from academic and health institutions from across the UK, Europe, Canada, Australia, Qatar, and South Africa. The MRC-University of Glasgow Centre for Virus […]

July 17, 2018
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What is weeSAM? weeSAM is a python script which produces coverage statistics and coverage plots from an input SAM or BAM file. Figures and stats are written up in HTML so users can easily view the coverage for their reference assembly. weeSAM is simple to run and the steps below give an illustration. What’s new […]

June 4, 2018
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This figure is an update of Figure 1 in “A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.” published by Zhang et al (2011). The figure was produced in SVG so you should be able to click on the name of the assembler which should take you straight to the […]

November 15, 2017
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A wide range of formats exist for representing the comparisons of different sequences to each other: blast tabular, blast xml, psl, pslx, SAM/BAM, BED Most of these formats can be converted from one format to another. Sometimes the format is lossless allowing for the original data to be perfectly converted without the loss of information. […]

October 23, 2017
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For the 3rd year running, we have held our Viral Bioinformatics and Genomics training course at the Garscube campus of the University of Glasgow. The course took place from Monday 7th August – Friday 11th August 2017, with 16 participants attending from academic and health institutions from across the UK, Europe, USA, Uganda, and Saudi […]

July 19, 2017
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FAST5 format from Oxford Nanopore (ONT) is in fact HDF5, which is a very flexible data model, library, and file format for storing and managing data. It is able to store an unlimited variety of datatypes. A number of tools have been developed for handling HDF5 available from here. The most useful are: hdfview, a […]

May 5, 2017
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Kraken is a really good k-mer based classification tool. I frequently use this tool for viral signal detection in metagenomic samples. A number of useful scripts such as updating Kraken databases are provided with the tool. Since the NCBI updated the FTP website structure and decided to phase-out Genbank Idenfiers (GIs), the default Kraken database update scripts […]

March 22, 2017
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The ONT produces results from sequencing run in the FAST5 format which is a variant of HDF5. “HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. HDF5 is […]

August 10, 2016
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We have shared our knowledge on Viral bioinformatics and genomics with yet another clever and friendly bunch of researchers. Sixteen delegates from across the world joined us for a week of intensive training. The line-up of instructors changed slightly due to the departure of Gavin Wilkie earlier in the year. Instructors: Joseph Hughes (Course Organiser) […]

6th Annual training course on Viral Bioinformatics and Genomics (21 – 25 August 2023)

4th Annual Training Course on Viral Bioinformatics and Genomics (20-24th Aug, 2018)

weeSAM version 1.5.

Extensive but not comprehensive compilation of de-novo assemblers

A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml

3rd Viral Bioinformatics and Genomics Training Course (7th – 11th August 2017)

Exploring the FAST5 format

Update Kraken databases

Extraction of FASTA sequences from Oxford Nanopore fast5 files – a comparison of tools

2nd Viral Bioinformatics and Genomics Training Course (1st – 5th August 2016)