Assembling draft genomes using contiBAIT

Kieran O'Neill, Mark Hills, Mike Gottlieb, Matthew Borkowski, Aly Karsan, Peter M. Lansdorp

OnderzoeksoutputAcademicpeer review

5 Citaten (Scopus)
175 Downloads (Pure)


A Summary: Massively parallel sequencing is now widely used, but data interpretation is only as good as the reference assembly to which it is aligned. While the number of reference assemblies has rapidly expanded, most of these remain at intermediate stages of completion, either as scaffold builds, or as chromosome builds (consisting of correctly ordered, but not necessarily correctly oriented scaffolds separated by gaps). Completion of de novo assemblies remains difficult, as regions that are repetitive or hard to sequence prevent the accumulation of larger scaffolds, and create errors such as misorientations and mislocalizations. Thus, complementary methods for determining the orientation and positioning of fragments are important for finishing assemblies. Strand-seq is a method for determining template strand inheritance in single cells, information that can be used to determine relative genomic distance and orientation between scaffolds, and find errors within them. We present contiBAIT, an R/Bioconductor package which uses Strand-seq data to repair and improve existing assemblies.

Originele taal-2English
Pagina's (van-tot)2737-2739
Aantal pagina's3
TijdschriftBioinformatics (Oxford, England)
Nummer van het tijdschrift17
Vroegere onlinedatum5-mei-2017
StatusPublished - 1-sep-2017

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