Workflow Wednesdays – Part 3. Read preprocessing – Read quality control 2. – QC results

26/06/2013

Text output Both FastQC and PRINSEQ can generate some basic statistics for each fastq file. For FASTQC these are the following: “Total Sequences” (i.e. the number of reads), “Filtered Sequences”, “Sequence Length” (read length range) and “%GC” (average GC-content). Additionally, tables for “Overrepresented sequences” and “Kmer content” are generated. PRINSEQ...

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 next...

Omixon at the European Society of Human Genetics conference in Paris!

23/06/2013

The Omixon team traveled again to a fantastic conference. This time our team went to Paris for the European Society of Human Genetics conference. The conference started during the afternoon of the 8th June at the huge Amphiteatre of Palais de Congrés with around 3000 geneticists from Europe.

Omixon on LinkedIn!

23/06/2013

We see amazing potential in using social media channels for spreading the word about next generation sequencing, HLA typing and bioinformatics in general. This is why we have been writing this blog, updating the Facebook and Twitter channels and now we open a new channel on LinkedIn. We hope to...

Flashcard Fridays – Comparison of variant callers

21/06/2013

A survey of tools for variant analysis of next-generation genome sequencing data. Pabinger et al. 2013 Following last week”s variant caller themed FF post, I will present you a very great article about variant detection and annotation. The paper gives a great review of basically every aspect of NGS based...