title: Sequence assembly.
abstract: Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and plays an important role in processing the information generated by these methods. Here, we provide a comprehensive overview of the current publicly available sequence assembly programs. We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html.
authors.affiliation: Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark.
authors.forename: K
authors.initials: K
authors.lastname: Scheibye-Alsing
authors.forename: S
authors.initials: S
authors.lastname: Hoffmann
authors.forename: A
authors.initials: A
authors.lastname: Frankel
authors.forename: P
authors.initials: P
authors.lastname: Jensen
authors.forename: P F
authors.initials: PF
authors.lastname: Stadler
authors.forename: Y
authors.initials: Y
authors.lastname: Mang
authors.forename: N
authors.initials: N
authors.lastname: Tommerup
authors.forename: M J
authors.initials: MJ
authors.lastname: Gilchrist
authors.forename: A-B
authors.initials: AB
authors.lastname: Nygård
authors.forename: S
authors.initials: S
authors.lastname: Cirera
authors.forename: C B
authors.initials: CB
authors.lastname: Jørgensen
authors.forename: M
authors.initials: M
authors.lastname: Fredholm
authors.forename: J
authors.initials: J
authors.lastname: Gorodkin
mesh_terms: D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000737:chemistry; D020224:Expressed Sequence Tags; D016678:Genome; D023281:Genomics / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D004247:DNA