GKNO.ME

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A bioinformatics pipeline launcher. Gkno opens the world of complex bioinformatic analysis to people of all level of computational expertise. This site contains documentation, tutorials and information on all the tools that comprise gkno. Learn how to download, install and maintain gkno and get data resources. Example: Call and visualize variants. Project allows visualization and real-time analysis of large data sets. Having generated variant calls for your sample, use vcf.iobio.

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gkno · tagline | gkno.me Reviews

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A bioinformatics pipeline launcher. Gkno opens the world of complex bioinformatic analysis to people of all level of computational expertise. This site contains documentation, tutorials and information on all the tools that comprise gkno. Learn how to download, install and maintain gkno and get data resources. Example: Call and visualize variants. Project allows visualization and real-time analysis of large data sets. Having generated variant calls for your sample, use vcf.iobio.

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gkno · tagline | gkno.me Reviews

https://gkno.me

A bioinformatics pipeline launcher. Gkno opens the world of complex bioinformatic analysis to people of all level of computational expertise. This site contains documentation, tutorials and information on all the tools that comprise gkno. Learn how to download, install and maintain gkno and get data resources. Example: Call and visualize variants. Project allows visualization and real-time analysis of large data sets. Having generated variant calls for your sample, use vcf.iobio.

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gkno.me

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Blog · gkno

http://gkno.me/blog.html

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· gkno

http://gkno.me/install.html

How to get gkno. Downloading and installing gkno is a very simple process, requiring only a few commands. To begin with, get the code using the following command:. Git clone https:/ github.com/gkno/gkno launcher.git. Running this command will download all of the gkno code and link in all of the tools that are part of gkno, but not actually download or compile the individual tools. To do this and make gkno operational, type the following command (this step will take a little while! Gkno freebayes -ps test.

3

How-to · gkno

http://gkno.me/how-to.html

How to use gkno. How to install gkno. How to find and use available gkno pipelines. Arguments applicable to all gkno. How to run gkno. In parallel or on a cluster. What are parameter sets and how are they used? In tool configuration files:. How to define parameter sets in tool configuration files? In pipeline configuration files:. How to define parameter sets in pipeline configuration files? Check that gkno pipelines are functioning correctly. Create your own parameter sets:. How to manipulate BAM files.

4

About us · gkno

http://gkno.me/about.html

We are a team of bioinformaticians and developers in the Marth lab at the USTAR Center for Genetic Discovery, Eccles Institute of Human Genetics in the University of Utah School of Medicine. If you have any comments, suggestions or questions, please contact us at AlistairNWard@gmail.com.

5

Pipelines · gkno

http://gkno.me/pipelines.html

Align single-end fastq files using BWA mem, converting the result to BAM. Align paired-end fastq files using BWA mem, converting the result to BAM. Align fastq files using Mosaik. In this version additional 'special' reference sequences are included (usually mobile element insertions) in the reference. Download a SnpEff database. Annotate a VCF file using SnpEff. Add or remove sample and read group information to a BAM file. Convert a BAM file back into a FASTQ file. Filter a set of BAM files. Search thr...

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bioinformatics.bc.edu

Scotty - You need more power!

http://bioinformatics.bc.edu/marthlab/scotty/scotty.php

Scotty - Power Analysis for RNA Seq Experiments. The official site for Scotty is now http:/ scotty.genetics.utah.edu/. This location however, remains functional. Scotty is a tool to assist in the designing of RNA Seq experiments that have adequate power to detect differential expression at the level required to achieve experimental aims. At the start of every experiment, someone must ask the question, "How many reads do we need to sequence? Please contact us if your require assistance. I have my own pilo...

ucgd.genetics.utah.edu

USTAR Center for Genetic Discovery » Software

http://ucgd.genetics.utah.edu/software

This page serves as an index for the applications written and distributed by the Yandell, Marth, and Quinlan labs. Each item may include links to: documentation, code, and publications. Software is listed with most recent releases first. VARPRISM (VARiant PRIoritization SuM). Annotates a VCF with any number of sorted and tabixed input BED, BAM, and VCF files in parallel. It does this by finding overlaps as it streams over the data and applying user-defined operations on the overlapping annotations. Genom...

marthlab.org

Software · MarthLab

http://marthlab.org/software.html

Provides both a programmers API and an end-users toolkit for handling BAM files. A Bayesian genetic variant detector designed to find small polymorphisms. A tool and pipeline management system to effectively deploy tools developed in the MarthLab as well as other third-party tools. GRAPH BASED VARIANT ADJUDICATION. A graph-based tool which performs local realignment to adjudicate and validate variant calls. REFERENCE FREE VARIANT DISCOVERY. Computational Framework for reconstructing tumor clone structures.

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gkno.me

gkno · tagline

A bioinformatics pipeline launcher. Gkno opens the world of complex bioinformatic analysis to people of all level of computational expertise. This site contains documentation, tutorials and information on all the tools that comprise gkno. Learn how to download, install and maintain gkno and get data resources. Example: Call and visualize variants. Project allows visualization and real-time analysis of large data sets. Having generated variant calls for your sample, use vcf.iobio.

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