Flashcard Fridays – nextgenseq@nature.com

30/08/2013

Similarly to last week’s “virtual issue” created by Bioinformatics (Oxford Journals), the Nature Group also has a selection of NGS related articles. This collection is available on their webpage. The list of highlighted articles is updated twice a month, and you can also subscribe to a monthly newsletter.

Workflow Wednesdays – Short read aligners – Omixon Variant Toolkit

28/08/2013

Omixon Variant Toolkit (aka Omixon Read Mapper or ORM)is our “own” alignment algorithm which is available as a standalone java application or in Omixon Target. The aligner actually contains two, slightly different algorithms*: one for shorter Illumina reads, called “bridge” and one for longer (IonTorrent and 454) reads, called...

Bioinformatics for Beginners – Bioconductor

26/08/2013

Bioconductor is an open source, open development toolset for analysing high-throughput genomic data. It is based on the R programming language (see last week’s post about R). Bioconductor can be used for a wide range of subjects from analysing assays, to querying databases or finding candidate binding sites for...

Workflow Wednesdays – Short Read Aligners – The “Oldies”

21/08/2013

Although BWA is a very popular and well tested aligner, it’s hardly the only aligner around. There is an extensive list of open source and commercial short read aligners available on Wikipedia. Another collection can be found on the EBI webpage (there’s also information about the number of citations...

Bioinformatics for Beginners – R

19/08/2013

No, today is not Talk Like A Pirate Day. “R” is a statistical software (more like an environment) which was inspired by “S” and was originally developed by Robert Gentleman and Ross Ihaka. Nowadays, more than a dozen contributors are working on development and bug fixes. There are also...