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 posed by the current surge of sequence data, with a focus on viral datasets and analyses. We will enable participants to understand and deal with high-throughput sequence (HTS) datasets and encourage the exchange of ideas and collaborations ..read more

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 Research (CVR) has been designated a World Organisation for Animal Health (OIE) Collaborating Centre for Viral Genomics and Bioinformatics at the 82nd OIE General Session. Instructors: Andrew Davison, Ana Filipe, Quan Gu (Course Organiser), Jose ..read more

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 in version 1.5? weeSAMv1.5 (https://github.com/centre-for-virus-research/weeSAM) is a python rewrite of Joseph Hughes’ weeSAMv1.4 written in perl and R. If you’re familiar with weeSAM all of the functionality of version 1.4 exists in 1.5 so no need to worry. The major changes / additio ..read more

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 PUBMED abstract. The size of the de-novo assembler names is relative to the number of citations in PUBMED. You can see that 2012 was the year of the De Brujin Graph assemblers. The post Extensive but not comprehensive compilation of de-novo assemblers appeared first on CVR Bioinforma ..read more

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. Other times, the format conversion is lossy permitting the conversion of only part of the original data resulting in the loss of some information. Here, I have compiled the tools or UNIX commands necessary for converting from one file format to another. As ..read more

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 Arabia. The course timetable was tweaked a little from the 1st and 2nd courses in previous years to include an introductory transcriptomics session, as well as poster and wine reception at the Centre for Virus Research (CVR). The course involved the usual suspec ..read more

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 java visual tool for viewing HDF5 files with some limited functionality of plotting data and the option of exporting subsets in HDF5 (extension .h5) h5ls, for listing specified entries of the HDF5 file h5dump, to examine the HDF5 file and export specified groups or datasets in ASC ..read more

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 do not work. So I decided to write a little python script to update Kraken databases that some Kraken users might find useful. This script automatically downloads: Human genome – most recent assembly version Complete bacterial referen ..read more

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 portable and is extensible, allowing applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and applications for managing, manipulating, viewing, and analyzing data in the HDF5 format.” from HDF group A number of tools have been developed for converting the ..read more

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) Andrew Davison Sejal Modha Richard Orton (co-organiser) Sreenu Vattipally Ana Da Silva Filipe The timetable changed a bit with more focus on advanced bash scripting (loops and conditions) as we asked the participants to have basic linux ..read more