This page provides a list of the scientific database available at OSC.
Bioinformatics & Biology
TrimGalore is a wrapper tool that automates quality and adapter trimming to FastQ files. It also provides functionality to RRBS sequence files.
FastQC provides quality control checks of high throughput sequence data that identify areas of the data that may cause problems during further analysis.
StringTie assembles aligned RNA-Seq reads into transcripts that represent splice variants in RNA-Seq samples.
Cufflinks is a program that analyzes RNA -Seq samples. It assembles aligned RNA-Seq reads into a set of transcripts, then inspects the transcripts to estimate abundances and test for differential expression and regulation in the RNA-Seq reads.
HISAT2 is a graph-based alignment program that maps DNA and RNA sequencing reads to a population of human genomes.
TopHat uses Bowtie, a high-throughput short read aligner, to analyze the mapping results for RNA-Seq reads and identify splice junctions.
Please note that tophat (and bowtie) cannot run in parallel, that is, on multiple nodes. Submitting multi-node jobs will only waste resources. In addition you must explicitly include the '-p' option to use multiple threads on a single node.
Kallisto is an RNA-seq quantification program. It quantifies abundances of transcripts from RNA-seq data and uses psedoalignment to determine the compatibility of reads with targets, without needing alignment.
FreeSurfer is a software package used to anaylze nueroimaging data.
Availability & Restrictions
The following versions of FreeSurfer are available on OSC clusters:
FSL is a library of tools for analyzing FMRI, MRI and DTI brain imaging data.
Availability and Restrictions
The following versions of FSL are available on OSC clusters: