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Extensive but not comprehensive compilation of de-novo assemblers

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 […]

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Exploring the FAST5 format

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 […]

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Setting up an Amazon ftp server to receive big files

Sharing large files with collaborators has rarely been a problem, we usually just compress them and put them on our web server and then send the link to our collaborator who can then download the file. However, we have struggled to find a solution to receive large files. We usually run out of space in […]

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BEAST in the cloud

We recently managed to set-up an account on amazon web service (AWS) that will enable us to test out how practical and efficient it will be to do computationally intensive analyses in the cloud. We often wonder whether it is worth spending loads of money on new servers and lots of time managing the hardware […]

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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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