The Sequence Read Archive (SRA Toolkit) stores raw sequence data from "next-generation" sequencing technologies including 454, IonTorrent, Illumina, SOLiD, Helicos and Complete Genomics. In addition to raw sequence data, SRA now stores alignment information in the form of read placements on a reference sequence. Use SRA Toolkit tools to directly operate on SRA runs.
The following versions of SRA Toolkit are available on OSC clusters:
RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files. The output consists of HTML reports and tab delimited files of metrics data. This program can be valuable for comparing sequencing quality across different samples or experiments to evaluate different experimental parameters. It can also be run on individual samples as a means of quality control before continuing with downstream analysis.
eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.
The following versions of eXpress are available on OSC clusters:
The Subread package comprises a suite of software programs for processing next-gen sequencing read data like Subread, Subjunc, featureCounts, and exactSNP.
The following versions of Subread are available on OSC clusters:
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.
The following versions of VCFtools are available on OSC clusters:
bcftools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.
The following versions of bcftools are available on OSC clusters:
VarScan is a platform-independent software tool developed at the Genome Institute at Washington University to detect variants in NGS data.
The following versions of VarScan are available on OSC clusters:
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.
The following versions of MuTect are available on OSC clusters:
Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
The following versions of Picard are available on OSC clusters:
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.
The following versions of SAMtools are available on OSC clusters:
