Computational and Bioinformatics Frameworks for Next-Generation Whole Exome and Genome Sequencing

Table 1

Program	Source type	Description	Website
Bowtie	Open source	Ungapped alignment	http://bowtie.cbcb.umd.edu/
		Refined use of FM Index using the BWT
		Fast and memory-efficient alignment
		Quality value output
Bowtie2	Open source	Extends Bowtie approach to be useful for gapped alignment	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
SEAL	Open source	Comparison of alignment algorithms using simulated short read sequencing runs	http://compbio.case.edu/seal/
SOAP3	Open source	Gapped and ungapped alignment	http://www.cs.hku.hk/2bwt-tools/soap3/; http://soap.genomics.org.cn/soap3.html
		Specialized for detecting and genotyping SNPs
		Hash table accelerates searching using BWT-based index
		Reports multiple possibilities rather than single best match
		Increased speed using GPU
BWA, BWA-SW	Open source	Most common/standard method used	http://maq.sourceforge.net/
		Index with BWT that is faster than the hash-based index used for MAQ
		Quality score reported
mrFAST, mrsFAST	Open source	Seed-and-extend alignment method with hash table inex for reference genome	—
		Reports all read mappings instead of single best mapping Useful for CNVs, structural variants
Novoalign	Commercially; available	Novocraft’s proprietary software with hashing strategy	http://www.novocraft.com/
		High accuracy for single end mapping
		Focused on sensitivity
SHRiMP/SHRiMP2	Open source	Specialized for SOLiD color-space reads using spaced seeds and SWA	http://compbio.cs.toronto.edu/shrimp/
		Also applicable for regular letter-space reads
		Handles higher level of polymorphisms
MAQ	Open source	Ungapped alignment	http://maq.sourceforget.net/
		Hash-based index with quality score for mapping
Stampy	Open source	Hybrid mapping algorithm and statistical model, complementary to BWA	http://www.well.ox.ac.uk/project-stampy/
ELAND	Commercially; available	Hash-based alignment program	http://www.illumina.com/
LAST aligner	Open source	Probablistic alignment quality scores as well as usual score matrix; Useful for preprocessing for SNP/indel calling	http://last.cbrc.jp/
SARUMAN	Open Source	Mapping approach for single-end reads that returns all possible alignments with given error threshold with high speed using GPUs	http://www.cebitec.uni-bielefeld.de/brf/saruman/saruman.html