Archives by date
You are browsing the site archives by date.
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’ [...]
This is a question that keeps cropping up on Seqanswers and Biostar. Amazingly there is still no 100% satisfactory pipeline for assembling combined Illumina and 454 data de novo. Here are the ways I know about: 1) Assemble 454 data on its own and correct with Illumina data For example, Newbler for the 454 data. [...]
I wanted to assess the quality of the assemblies that you might expect to get from assembling Ion Torrent reads de novo for bacterial genomes (see my last post for the initial results of assembly). By good fortune, Aaron Darling of Mauve fame just published a manuscript in Bioinformatics describing Mauve Assembly Metrics. For those [...]
I am getting tired of having to examine sub-standard PhD theses and then having to write the same old comments in the report on the thesis, so I have decided to set down the minimum requirements for a PhD thesis. Anyone who is contemplating asking me to examine a thesis should read these and comply [...]
Ion Torrent have released a set of longer read 314 data, along with this technical note. (Graphic from PRINSEQ) The reads are indeed much longer than we have seen with our previous 316 runs, with a mean of 223bp and longest read being 398bp. Curiously this longer-read protocol has been done on a 314 chip [...]