BCFtools
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.
Availability and Restrictions
Versions
The following versions of BCFtools are available on OSC clusters:
Ascend
Picard
Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Availability and Restrictions
Versions
The following versions of Picard are available on OSC clusters:
SAMtools
SAM format is a generic format for storing large nucleotide sequence alignments. SAMtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
Availability and Restrictions
The following versions of SAMtools are available on OSC clusters:
GATK
GATK is a software package for analysis of high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance.
Availability and Restrictions
Versions
The following versions of GATK are available on OSC clusters:
Bowtie
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).
Availability and Restrictions
Versions
The following versions of Bowtie1 are available on OSC clusters:
bedtools
Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. While each individual tool is designed to do a relatively simple task, quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.
Availability and Restrictions
Versions
The following versions of bedtools are available on OSC clusters:
HOWTO: Identify users on a project account and check status
An eligible principal investigator (PI) heads a project account and can authorize/remove user accounts under the project account (please check our Allocations and Accounts documentation for more details). This document shows you how to identify users on a project account and check the status of each user.
Linaro Performance Reports
Linaro Performance Reports is a simple tool used to generate a single-page HTML or plain text report that presents the overall performance characteristics of HPC applications. It supports pthreads, OpenMP, or MPI code on CPU, GPU, and MIC based architectures.
OpenMPI
MPI is a standard library for performing parallel processing using a distributed memory model. The Pitzer, Ascend, and Cardinal clusters at OSC can use the OpenMPI implementation of the Message Passing Interface (MPI).
Software Refresh
OSC timely installs new software versions on OSC systems, and periodically do coordinated software refresh (update the default versions to be more up-to-date and remove some versions that are quite out of date) on OSC systems. While we encourage everyone to use up-to-date software, the old defaults will still be available till the next software refresh, in case some users prefer to use the old defaults. The software refresh is usually made during the scheduled downtime, while we will send out notifications to all users ahead of time for any questions/suggestions/concerns.
