Disclaimer – The following public and NC State resources are listed for help in bioinformatic analysis, and are meant to be a resource guide for the greater research community. It is worth noting, however, that use of these resources, without full knowledge of the appropriate procedures and necessary experimental designs, could lead to misleading or spurious results. The GSL highly recommends consultation with the NCSU Bioinformatic Consulting & Service Core, who can provide a free initial consultation for first time users upon request.

Consulting & Data Analysis


  • NCSU Bioinformatic Consulting & Service Core – The BCSC offers expertise in analysis of data related to genetics and genomics. Services are available to all members of the North Carolina State University community, as well as the research community at large.

Hardware Resources


NCSU Users

Public Access

Fee for Use

Software Resources


NCSU Users

  • OIT High Performance Computing – IBM Blade Center Linux Cluster (henry2) with LSF job submission. MAKER genome annotation, PBJelly, Trinity, Velvet/Oases, SOAPdenovo2, MrBayes, FastXToolkit, Bowtie2, TopHat, Cufflinks, GenomeTools, SAMTools, PacBio SMRT analysis, and much more!

Open Access/Freeware

  • Bioconductor – An R-based statistical platform for analyzing high-throughput genomic data.
  • CyVerse Discovery Environment – BLAST/BLAT, BEDtools, CEGMA, MetaGeneMark, InterProScan, BWA, Bowtie, SAMTools, FastX toolkit, GBS workflows, and much more!
  • Galaxy – FastQC, FastQ conversions, Bowtie2, BWA, Tophat, Cufflinks, Cuffdiff, SAMtools, BAMtools, and much more!
  • CIPRES – RAxML; MrBayes; BEAST; BEAST2; GARLI; MAFFT; DPPDIV; FastTree, jModelTest2, Migrate-N, PAUP*, Poy, ClustalW, Contralign, MUSCLE, PROBCONS, PROBALIGN
  • UGENE – Free Java-based NGS pipeline for variant calling, RNA-seq, and ChIP-seq data analysis.
  • WEKA – Open-source machine-learning algorithms for data mining.
  • DAVID – Online gene-enrichment and functional pathway analysis tool.
  • MOTHUR – Open-source software for microbial ecology and metagenomics.
  • MG-RAST – An automated analysis platform for metagenomics.
  • QIIME – A bioinformatics pipeline for performing microbiome analysis.
  • Open-Source List – A general list of open-source bioinformatics software packages.
  • Trimmomatic – A flexible read trimming tool for Illumina NGS data.
  • FastQC – A Java based software for assessing read quality
  • Nephele – NIH supported microbiome analysis pipeline – NEW!
  • One Codex – data platform for applied microbial genomics – NEW!

Learning Resources


Select NCSU Courses (many great courses available)

GN 427Introductory BioinformaticsDr. David Reif
BIT 815Deep Sequencing Data AnalysisDr. Ross Whetten
BIT 495/595MetagenomicsDr. Carlos Goller
ST590ABioinformatics IDr. Spencer Muse, Dr. Hamid Ashrafi, and Dr. Fred Wright
ANS 575 Current Topics in Genomics and Proteomics in Animal ScienceDr. Sunny Liu

Mini-Courses

  • NCSU BRC Short Courses
  • Coursera – Bioconductor for Genomic Data Sciences, Genomic Data Sciences with Galaxy, Command Line Tools for Genomic Data Analysis
  • Edx – ChIP-seq data analysis, RNA-seq data analysis, DNA methylation data analysis

Other References