bam2fastq
bam2fastq is used to extract raw sequences (with qualities) from programs like SAMtools, Picard, and Bamtools.
Availability and Restrictions
Versions
The following versions of bam2fastq are available on OSC clusters:
Pitzer
SRA Toolkit
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.
Availability and Restrictions
The following versions of SRA Toolkit 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:
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:
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:
