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:
Software
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:
BWA
BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM.
Availability and Restrictions
Versions
The following versions of BWA are available on OSC clusters:
Bowtie1
Bowtie1 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:
NWChem
NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.
Availability and Restrictions
Versions
The following versions of NWChem are available on OSC clusters:
Linaro MAP
Linaro MAP is a full scale profiler for HPC programs. We recommend using Linaro MAP after reviewing reports from Linaro Performance Reports. MAP supports pthreads, OpenMP, and MPI software on CPU, GPU, and MIC based architectures.
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.
