Bioinformatics tools for VCF files

With the ever growing abundance of Next Generation Sequencing (NGS) data there continues to be a challenge faced by the research community to not only standardize best practices and analysis methods, but to embrace the foray of open-source tools and file formats. Having been engaged since almost the beginning of this NGS data outburst with [...]


The Ebola outbreak of 2014 (Contd.)

Following up on the previous post here are some more detail on the recent Science paper along with a round-up of "what do we know, what have we learned" thus far. The Gire et al paper in Science was huge amount of work and a giant collaborative research effort. Being a computational biology researcher, I [...]

Solving the Ebola Virus Genome and Identifying Possible Diagnosis

If you have ever played the card game Killer Bunnies and your Bunnies in the Bunny circle have died because of the Level 11 Weapon of Ebola Virus you want to read this. Research community is making strides to understand whether the virus is adapting to its host or changing as it spreads through the [...]

Exomes vs Genomes (re-visited)

The paper by Lupski et al in Genome Medicine provides fuel to the perpetual debate of Whole Exome Sequencing (WES) vs Whole Genome Sequencing (WGS). It takes me down the memory lane to my own presentation "Genomes or Exomes: evaluation of cost, time and coverage" at Beyond the Genome 2011 conference. (If you would like [...]

Mitochondrial Gold Rush

Mitochondrial genomes can be extracted from Whole Exome Sequencing (WES) data as outlined by this paper in Nature methods by Ernesto Picardi & Graziano Pesole. Tools like Mito Seek are now available that gather mitochondrial read sequences from NGS data and perform high throughput sequence analysis. Availability of mitochondrial genomes is important as genomic variation in mitochondria has [...]

Journal Club: Indels in 179 genomes (1000genome data)

The origin, evolution and functional impact of short insertion-deletion variants identified in 179 human genomes Genome Research Finally there is a comprehensive analysis on indels, and of course it is the Next Generation Sequencing data that is driving it. I have my concerns with the biases of NGS technology and analysis along with ensuing false-positives [...]

AGBT 2013 Saturday sessions

Plenary Session: Genomic Technologies Len Pennacchio, Lawrence Berkeley National Laboratory, Chair -- could not take notes on some of the talks and afternoon session 9:00 a.m. – 9:30 a.m. Rebecca Leary, Johns Hopkins Kimmel Cancer Center “Personalized Approaches to Non-invasive Cancer Detection” - personalized analysis of rearranged ends (PARE)-identify structural alterations in solid tumors - [...]