TABLE 3.
A Partial List of Bioinformatics Programs Used to Analyze Next Generation DNA Sequencing Data
| Program | Primary utility | Web address |
|---|---|---|
| SAMtools | A commonly used alignment format files 103 | http://samtools.sourceforge.net/ |
| The Genome Analysis Toolkit (GATK) | A structured programming framework designed to enable rapid development of efficient and robust analysis tools for next-generation DNA sequencers 104 | http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome Analysis_Toolkit |
| BWA | A fast light-weighted tool that aligns short sequences to a sequence database, such as the human reference genome. | http://bio-bwa.sourceforge.net/ |
| Novocraft | Commercial tools for reference alignment of paired-end and single-end for Illumina, Solid and 454 | http://www.novocraft.com/main/index.php |
| BFAST | Blat-like Fast Accurate Search Tool 105 | http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page |
| Bowtie | Ultrafast, memory-efficient short read aligner 106 | http://bowtiebio.sourceforge.net/index.shtml |
| ANNOVAR | Functionally annotate genetic variants detected from diverse genomes 107 | http://www.openbioinformatics.org/annovar/ |
| SequenceVariant Analyzer (SVA) | A software to annotate, visualize, and analyze the genetic variants identified through NGS | http://www.svaproject.org/ |
| Integrative Genomics Viewer (IGV) | A high-performance visualization tool for interactive exploration of large, integrated datasets 108 | http://www.broadinstitute.org/software/igv/home |
| UCSC Genome Browser | Web-based tools to integrate, visualize and analyze genomics and clinical data 109 | http://genome.ucsc.edu/ |
Courtesy of Manuel Gonzalez-Garay, Ph.D. at Center for Cardiovascular Genetics, The University of Texas Health Science Center, Houston, TX.