FastQC
FastQC provides quality control checks of high throughput sequence data that identify areas of the data that may cause problems during further analysis.
Ascend
Perl
Perl is a family of programming languages.
Cufflinks
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
HISAT2 is a graph-based alignment program that maps DNA and RNA sequencing reads to a population of human genomes.
Apptainer (formerly Singularity)
Apptainer (formerly Singularity) is a container system designed for use on High Performance Computing (HPC) systems. It allows users to run both Docker and Singularity containers.
HTSlib
HTSlib is a C library used for reading and writing high-throughput sequencing data.
RELION
RELION (REgularised LIkelihood OptimisatioN) is a stand-alone computer program for the refinement of 3D reconstructions or 2D class averages in electron cryo-microscopy.
We have identified some issues with the RELION installations. For more details, please refere the "Known Issues" section below.
To address the issues, we have decided to deprecate affected versions, including: relion/3.1, relion/3.1-gpu, relion/3.1.3, relion/4.0.0, and relion/4.0b on Pitzer. Additionally, we will deprecate other versions that are rarely used to improve maintenance. These versions include relion2/2.0 and relion/3.0.4.
The deprecation action was done on January 23, 2024. To migrate your jobs, please refer to the "Versions" table below for available versions. If you require any assistance, please contact OSC help.
To address the issues, we have decided to deprecate affected versions, including: relion/3.1, relion/3.1-gpu, relion/3.1.3, relion/4.0.0, and relion/4.0b on Pitzer. Additionally, we will deprecate other versions that are rarely used to improve maintenance. These versions include relion2/2.0 and relion/3.0.4.
The deprecation action was done on January 23, 2024. To migrate your jobs, please refer to the "Versions" table below for available versions. If you require any assistance, please contact OSC help.
FreeSurfer
FreeSurfer is a software package used to anaylze nueroimaging data.
Availability & Restrictions
Versions
The following versions of FreeSurfer are available on OSC clusters:
HOWTO: Use Docker and Apptainer/Singularity Containers at OSC
It is now possible to run Docker and Apptainer/Singularity containers on all clusters at OSC. Single-node jobs are currently supported, including GPU jobs; MPI jobs are planned for the future.
From the Docker website: "A container image is a lightweight, stand-alone, executable package of a piece of software that includes everything needed to run it: code, runtime, system tools, system libraries, settings."
FSL
FSL is a library of tools for analyzing FMRI, MRI and DTI brain imaging data.
Availability and Restrictions
Versions
The following versions of FSL are available on OSC clusters:
