Bioinformatics for Beginners – File formats: Part 1. Reference sequences

24/06/2013

The most widely used file format for reference sequences is the fasta format. Both nucleotide and protein sequences can be represented in fasta format. A fasta formatted file begins with a single-line description, followed by the sequence data. The description line starts with a greater-than (“>”) symbol. In the...

Omixon’s upcoming HLA typing webinar

20/06/2013

Broadcast date: 3rd July 2013, Wednesday Time: 12.00-1.00 PM EDT/ 18.00-19.00 CET Come and join our CEO, Attila Berces online in a presentation and demo of how Omixon Target HLA typing will bring you value during the analysis of NGS data. Our guest speaker is Dr. Dimitri Monos, University of Pennsylvania and The Children”s...

Workflow Wednesdays – Part 3. Read preprocessing – Read quality control 1. – Running QC tools

19/06/2013

Read quality control tools can provide very useful information about the the success of your sequencing experiment, without the need to run time consuming alignments and variant calls. Based on read length, per base quality, base content and other basic statistics you can find out a lot about your...

Bioinformatics for Beginners – How to get NGS data? Part 2. Reference sequences

17/06/2013

The most obvious (and probably the most used) source of reference sequences (or any kind of sequences) is the NCBI Nucleotide database and its “sister” sites: the EBI European Nucleotide Archive, and the DNA Data Bank of Japan. All three sites provide some kind of search functionality and a...

Flashcard Fridays – Part 2. Let’s talk about variant callers!

14/06/2013

If you’re interested in the underlying algorithm of variant callers, it’s always a safe bet to check out the paper(s) about the variant caller. So here are the papers for the two most commonly used variant callers: