A Case for Long CIGARs: Achieving 50% Compression of BAM Files

I am studying NA06984.454.MOSAIK.SRP000033.2009_11.bam. Not to find SNPs, structural variations, or derive any biological insights into the CEU population – but simply from an IT storage perspective. How much disk space is really needed to store the entire information of the 1.23 million matches present in this 151 Mb file? If I can get to … Continue reading “A Case for Long CIGARs: Achieving 50% Compression of BAM Files”

Introducing COBWeb – our read alignment algorithm

The upcoming release of Avadis NGS 1.3 provides support for aligning raw reads to the genome – for small RNA, ChIP-Seq and DNA-Seq experiments. The alignment program integrated with Avadis NGS is a new proprietary algorithm called COBWeb. The name loosely comes from the approach we took to developing the algorithm – a computationally-optimized Burrows … Continue reading “Introducing COBWeb – our read alignment algorithm”

Welcome to our blog

Our goal for this blog is to be a distraction that is useful for you as well as for us. We will use this venue to express our bewilderment and discoveries as we traverse the genome. Mostly, we’ll geek out over puzzling challenges in bioinformatics, but we may also delve into other relevant topics – … Continue reading “Welcome to our blog”