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 [...]

Advertisements

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 [...]

Venn Diagrams Simplified

Not a week goes by without me having to compare multiple lists to evaluate overlap. Re-analyzing any data and comparing that with previously computed data, comparing results from multiple tools or multiple samples. Sometimes the unix commands diff, paste and join come handy, but most times am looking for some additional information. Almost always, am [...]