[Retracted] Next Generation Sequencing: Potential and Application in Drug Discovery
Table 1
Important bioinformatics tools for analysis of NGS data.
Alignment, assembly, and visualization tools: Velvet (http://www.ebi.ac.uk/~zerbino/velvet/): tool for de novo assembly of short and paired reads. EULER (http://ngslib.i-med.ac.at/node/64): tool to generate short-read assembly and facilitate assembly of combined reads of NGS and Sanger sequencing. GMAP (http://www.gene.com/share/gmap): program to map and align cDNA sequences to genome sequence using minimal time and memory and facilitates batch processing.
Sequence variant discovery tools: SNPsniffer tool for SNP discovery specifically designed for Roche/454 sequences. SeqMap (http://www-personal.umich.edu/~jianghui/seqmap/): tool to map short sequences to a reference genome and detect multiple substitutions and indels.
Integrated tools: NextGENe (http://www.softgenetics.com/NextGENe.html): software to analyze NGS data for de novo assembly, SNP and indel detection, and transcriptome analysis. SeqMan genome analyzer (http://www.dnastar.com/products/SMGA.php): software with capacity to align NGS and Sanger data and detect SNPs and also facilitates visualization. CLCbio Genomics Workbench (http://www.clcbio.com): tool for de novo and reference assembly of Sanger and NGS sequence data, SNP detection and browsing.
