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Ascend, Cardinal, Pitzer
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:
Cardinal
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:
Ascend, Cardinal, Pitzer
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:
Ascend, Cardinal, Pitzer
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, Cardinal, Pitzer
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:
Ascend, Cardinal, Pitzer
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:
Ascend, Cardinal, Pitzer
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:
Cardinal, Pitzer
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:
Ascend, Cardinal, Pitzer
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:
Ascend, Cardinal
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.
