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.
Bioinformatics & Biology
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.
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.