Initially, gkno grew out of an internal need to share pipelines (and knowledge) between lab members while working on the 1000 Genomes project. gkno is a set of tools and a framework to link tools together into analyses pipelines. It includes pipelines that we have developed during our daily work on large scale sequencing projects. Additionally, documentation and tutorials are provided to allow users of any experience level to utilize these resources.
We took inspiration from our own subway system here in Boston ( the T ) to create pipeline maps. Just as the T map helps you get from point A to point B, the pipeline maps help you take what you have (e.g a fastq file) and get to where you want to go (e.g. a vcf) while clearly illustrating all the stops along the way.
It's All About The Settings!
Choosing the correct settings for your data is often overlooked, but it's one of the trickiest aspects of generating meaningful results. To help, we have created some guidelines and tutorials to better utilize your software. We highly recommend reading analysis 101.
gkno uses biostars.org as an open forum to allow all gkno users to provide support and share best practices. More Info
Who we are
We are a group of tool developers from the Marthlab at Boston College. We create software for the analysis of next-generation sequencing data. You can read more about our work, publications, and research opportunities on our lab homesite.