Bioinformatics

Software and Services

Freely available bioinformatics software is maintained in the bioinfo file in the Beocat home directory /homes/bioinfo/bioinfo_software. You can add any of the available updated bioinformatics software, including BioPerl, to your environment by running the command "source /homes/bioinfo/bioinfo-software-env.cshrc" at the athena command prompt, after you have logged onto Beocat. For a complete list of available software type "ls /homes/bioinfo/bioinfo-software/".

i5K-INBRE GitHub Organization The Bioinformatics Core contributes custom scripts from common NGS analysis to our K-INBRE i5K Github script sharing organization. Below is a list of repositories in our Github Organization:

 

 

 

 

transcriptome-and-genome-assembly - Scripts in this repository have been used to assemble de novo transcriptomes and genomes


RNA-Seq-annotation-and-comparison - Scripts to test for differential expression or annotate transcripts

read-cleaning-format-conversion - These scripts are fastq and fasta file tools for cleaning or filtering

Irys-scaffolding - Scripts to parse IrysView output

genome-annotation-and-comparison - Scripts to generate summary metrics for genomes refine genome annotations

ngs_pipelines_on_beocat The Bioinformatics Core and our collaborators in the Olson Lab are developing easy to use NGS Analysis Pipelines for Beocat. Each pipeline has a tutorial that explains how to import a sample dataset, clean reads, perform analysis, and summarize results. Below is a brief description of the pipelines for a more detailed list go to http://i5k-kinbre-script-share.github.io/transcriptome-and-genome-assembly/:

AssembleG - Multi k-mer de novo genome assembly with AbYSS. Tutorial: https://github.com/i5K-KINBRE-script-share/transcriptome-and-genome-assembly/blob/master/KSU_bioinfo_lab/AssembleG/AssembleG_LAB.md

AssembleT - Multi k-mer de novo transcriptome assembly with Oases. Tutorial: https://github.com/i5K-KINBRE-script-share/transcriptome-and-genome-assembly/blob/master/KSU_bioinfo_lab/AssembleT/AssembleT_LAB.md

RNA-SeqAlign2Ref - align reads to a reference genome with Tophat2 and test for differential expression using Cuffdiff2. Tutorial: https://github.com/i5K-KINBRE-script-share/RNA-Seq-annotation-and-comparison/blob/master/KSU_bioinfo_lab/RNA-SeqAlign2RefREADME.md

Services and Support

The KSU Bioinformatics Center is currently funded by the K-INBRE. Thus, we are able to provide the following services and consultation for a reduced charge to researchers in the K-INBRE network. Researchers who are preparing grant proposals may also contact us for a description of our facilities and services.

However, for grant proposals in which bioinformatics will be an integrated component, we would suggest that you consider collaborative research. In these cases, we will be glad to participate in proposal preparation, and specialized persons may be assigned to work on the project (if funded).

Available Services

- We provide assistance with installation and maintenance of various bioinformatics software packages.

- We provide services in sequence raw data processing, assembly and preliminary annotation.

- We can assist you in sequence analysis, including BLAST search, protein domain analysis, multiple sequence alignment, phylogenetic analysis, and other common sequence-based methods.

- We provide assistance in microarray data normalization, transformation and basic statistical tests using the GeneSpring software package.

- We provide consultation on biological data acquisition and database design.