title: SeqMap: mapping massive amount of oligonucleotides to the genome.
abstract: SeqMap is a tool for mapping large amount of short sequences to the genome. It is designed for finding all the places in a reference genome where each sequence may come from. This task is essential to the analysis of data from ultra high-throughput sequencing machines. With a carefully designed index-filtering algorithm and an efficient implementation, SeqMap can map tens of millions of short sequences to a genome of several billions of nucleotides. Multiple substitutions and insertions/deletions of the nucleotide bases in the sequences can be tolerated and therefore detected. SeqMap supports FASTA input format and various output formats, and provides command line options for tuning almost every aspect of the mapping process. A typical mapping can be done in a few hours on a desktop PC. Parallel use of SeqMap on a cluster is also very straightforward.
authors.affiliation: Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, USA.
authors.forename: Hui
authors.initials: H
authors.lastname: Jiang
authors.forename: Wing Hung
authors.initials: WH
authors.lastname: Wong
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D017353:Gene Deletion; D016678:Genome; D023281:Genomics; D016254:Mutagenesis, Insertional; D009841:Oligonucleotides / Q000737:chemistry*; D012984:Software
chemical_list: D009841:Oligonucleotides