eXpress
eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.
Availability and Restrictions
Versions
The following versions of eXpress are available on OSC clusters:
Ncview
Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc.
Availability and Restrictions
Versions
The following versions of Ncview are available on OSC clusters:
Subread
The Subread package comprises a suite of software programs for processing next-gen sequencing read data like Subread, Subjunc, featureCounts, and exactSNP.
Availability and Restrictions
Versions
The following versions of Subread are available on OSC clusters:
VCFtools
VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
Availability and Restrictions
The following versions of VCFtools are available on OSC clusters:
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:
VarScan
VarScan is a platform-independent software tool developed at the Genome Institute at Washington University to detect variants in NGS data.
Availability and Restrictions
Versions
The following versions of VarScan are available on OSC clusters:
MuTect
MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.
Availability and Restrictions
Versions
The following versions of MuTect are available on OSC clusters:
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: