Metagenomics

Methods for taxonomic assignment of shotgun whole-genome metagenomics reads

Part of an introductory course on whole-genome shotgun metagenomic sequence analysis, I thought it might be useful to reproduce here. I am working on building a regularly updated PAUDA and LAST index of microbial-RefSeq protein sequences that might be useful for those who would like to save some time, or don’t have enough memory to […]

COST training school: Bioinformatics for microbial community analysis

I will be helping teach one day of this course which is fully-funded if you are a student from a COST-participating country… see below for details: Deadline is next week, so hurry if you are interested. COST training school ES1103: Bioinformatics for microbial community analysis Dates: December 11th- 14th (the school will begin at 1pm […]

Sequencing low diversity libraries on Illumina MiSeq

After its launch in 2005, the 454 rapidly became the go-to technology if you wanted to sample diversity in amplicon libraries, whether a cancer panel, a viral quasispecies or microbial community profiling. It is not difficult to see why. Compared to Sanger sequencing the 454 offered massive throughput, being able to produce over a million reads […]

Research Fellow in Microbial Bioinformatics

Research Fellow Microbial Bioinformatics University of Birmingham - School of Biosciences Salary: from £27,428 to £37,990 a year Fixed term: until 31 July 2016 Closing date: 17 December 2011 Reference: 47410 Applications are invited for a Research Fellow position devoted to bioinformatics support and research in the field of high-throughput sequencing and the microbiology of trauma patients. This exciting opportunity […]

Live Tweets from Applying Advanced Molecular Techniques to Healthcare Infection Day 3

Here is a crude file dump of my live tweets from the third day of the Applying Advanced Molecular Techniques to Healthcare Infection. Same caveats as before: apologies for extraneous material, but something better than nothing. Also have created newspaper of links from the meeting here: http://paper.li/mjpallen/1319610603 #AAMTHI am signing off live tweeting and will start […]

Are diagnostic and public health bacteriology ready to become branches of genomic medicine?

This article of ours has just appeared in Genome Medicine. Pallen and Loman Genome Medicine 2011, 3:53 http://genomemedicine.com/content/3/8/53 MUSINGS: Are diagnostic and public health bacteriology ready to become branches of genomic medicine? Mark J Pallen* and Nicholas J Loman Diagnostic medical bacteriology is a conservative discipline. When busy house officers scribble ‘M, C & S’ […]