Table 1.
Software tools and algorithms for alignment, SAM/BAM integration, copy number estimation, SV detection, and de novo assembly using NGS data
| Software | Description | URL |
|---|---|---|
| Read alignment/mapping | ||
| Maq | Widely used mapping algorithm for short NGS reads | http://www.maq.sourceforge.net |
| BWA/BWASW | Burrows-Wheeler Aligner for mapping short (bwa) or long (bwasw) reads | http://www.bio-bwa.sourceforge.net |
| Bowtie | Ultrafast short read aligner for Illumina data | http://www.bowtie-bio.sourceforge.net |
| BFAST | Customizable BLAT-like read mapping tool for NGS data | http://www.genome.ucla.edu/bfast |
| SHRiMP | Efficient Smith-Waterman aligner for short read data | http://www.compbio.cs.toronto.edu/shrimp |
| SOAP | Short oligo analysis package for alignment and variant calling | http://www.soap.genomics.org.cn/ |
| mrFAST | Maps read to all possible locations for duplication/CNV detection. | http://www.mrfast.sourceforge.net |
| SSAHA2 | Sequence Search and Alignment by Hashing Algorithm | http://www.sanger.ac.uk/resources/software/ssaha2 |
|
| ||
| SAM/BAM file operations | ||
| SAMtools | A suite of tools for manipulating NGS data in SAM/BAM format | http://www.samtools.sourceforge.net |
| Picard | A suite of Java tools for validating and de-duplicating SAM/BAM files | http://www.picard.sourceforge.net |
|
| ||
| Copy number estimation | ||
| EWT | CNV calling with event-wise testing (EWT) | http://www.genome.cshlp.org/content/19/9/1586 |
| SegSeq | CNV calling with local changepoint analysis and merging | http://www.broad.mit.edu/cancer/pub/solexa_copy_numbers |
| CMDS | Recurrent CNA calling in sample populations | https://www.dsgweb.wustl.edu/qunyuan/software/cmds |
|
| ||
| Structural variation detection | ||
| BreakDancer | SV prediction tool for paired-end Illumina data | http://www.genome.wustl.edu/tools/cancer-genomics |
| GASV | Geometric method for SV detection | http://www.cs.brown.edu/people/braphael/software.html |
| Pindel | Indel prediction tool for paired-end NGS data | http://www.ebi.ac.uk/~kye/pindel |
|
| ||
| De novo assembly | ||
| ABySS | A de novo, parallel, paired-end sequence assembler for short reads | http://www.bcgsc.ca/platform/bioinfo/software/abyss |
| Velvet | A de novo sequence assembler for short reads | http://www.ebi.ac.uk/~zerbino/velvet |
| TIGRA | De novo assembly of SV breakpoints | http://www.genome.wustl.edu/ |
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| ||
| Visualization | ||
| Circos | Circular visualization of genome and comparative genomics data | http://www.mkweb.bcgsc.ca/circos/ |
| IGV | BAM-driven integrative genomics viewer for NGS data | http://www.broadinstitute.org/igv |
| LookSeq | Web-based tool for visualization and analysis of sequence alignments | http://www.sanger.ac.uk/resources/software/lookseq |
| Pairoscope | BAM-driven visualization of predicted structural variants | http://www.pairoscope.sourceforge.net |
| Savant | Desktop visualization tool that represents paired-end reads for SV identification. | http://www.compbio.cs.toronto.edu/savant |