The release date for the next version of Avadis NGS is just around the corner. Not only does the software include a lot of refinements in some of the older features, but it also boasts of a number of cool new ones! So here is a sneak peak at some of these features in version 1.5.
As a cancer biologist I am really looking forward to the new Copy Number Detection tool. The discovery in the last decade that CNVs are very common in the human genome, with a frequency greater than 10%, has changed how biologists perceive their importance. This means that in addition to SNPs and Indels, these larger structural variations in human or even in say mouse DNA, could explain the amazing diversity within each species. CNVs can totally disrupt the transcription of genes, either with the deletion/duplication of the gene, or by the disruption of its regulatory site. For this reason, several research groups across the world are trying to connect the dots between CNVs and disease/cancer loci. The Avadis NGS team is particularly excited about the copy number workflow, because it corrects data for sample ploidy and also for contamination by normal cellular material in tumor samples. This will provide better estimates of CNV regions in the genome. Certainly a tool worth watching out for!
The team has also tried to make more pipelines available to the end-user, allowing compute-intensive jobs to run in the background. So one could potentially be running a complete workflow from raw-read alignments (for DNA-Seq, RNA-Seq or ChIP-Seq) to variant calling in these automated pipelines, and writing a blog at the same time!
Another feature that is a particular favorite of mine is an Elastic Genome Browser that the Avadis team has come up with. Who doesn’t appreciate good visualization of data? Remember how we nodded off when someone presented a seminar with too many text slides? The new elastic genome browser visualization tool in version 1.5 allows a user to look at multiple genomic regions simultaneously. So if you are looking at data to identify gene fusions, novel splices or large structural variations, this tool will help you put all the information on one screen, and will also let you look at only those regions that interest you.
For those users heavily invested in DNA sequencing, the software has been upgraded considerably. It performs additional pre-processing steps such as local realignment and base quality score recalibration. While local realignment will ensure that sequenced reads have fewer alignment artifacts, both these refinements will help reduce false positives. Overall, the workflow will result in improved variant calling.
And last but by no means the least, the Avadis NGS team has turned a nice trick with the Alignment tool. In the new version, the tool can run faster by a factor of 2 on machines with memory capacities of 8GB or more. In case of DNA alignment, the new version further speeds up the computation by utilizing the SSE feature of the processor architecture.
I am really excited about all these features and can’t wait to see them all come together!