metilene is a software tool to annotate differentally methylated regions (DMRs) and differentially methylated CpG sites (DMCs) from Methyl-seq data. metilene accounts for intra-group variances and offers different modes de-novo DMR detection, DMR detection within a known set of genomic features, and DMC detection. Various biological data can be used, metilene works with Whole-genome Bisulfite Sequencing (WGBS), Reduced representation bisulfite sequencing (RRBS), and any other input data, as long as absolute (methylation) levels and genomic coordinates are provided.
Bioinformatics & Biology
Rosetta is a software suite that includes algorithms for computational modeling and analysis of protein structures.
Desmond is a software package that perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters, general-purpose supercomputers, and GPUs. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer.
OSC is refreshing the software stack for Owens and Ruby on September 4, 2018. This will be done by a rolling reboot. During the software refresh, some default versions are updated to be more up-to-date. Information about the old and new default versions, as well as all available versions of each software package will be included on the corresponding OSC software webpage. See https://www.osc.edu/supercomputing/software-list.
Microbial Genomes is a database of prokaryotic genome sequencing project data.
Availability and Restrictions
Microbial Genomes is available on the Owens cluster. The versions currently available at OSC are:
OSC periodically updates The NCBI BLAST database.
BLAST database is available on the Owens and Oakley clusters. The versions currently available at OSC are:
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.