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Improves Early Build Genome Assemblies using Strand-Seq Data

Bioconductor version: Release (3.19)

Using strand inheritance data from multiple single cells from the organism whose genome is to be assembled, contiBAIT can cluster unbridged contigs together into putative chromosomes, and order the contigs within those chromosomes.

Author: Kieran O'Neill, Mark Hills, Mike Gottlieb

Maintainer: Kieran O'Neill <koneill at>

Citation (from within R, enter citation("contiBAIT")):


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Reference Manual PDF


biocViews CellBasedAssays, Genetics, GenomeAssembly, ImmunoOncology, QualityControl, Software, WholeGenome
Version 1.32.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License BSD_2_clause + file LICENSE
Depends BH (>= 1.51.0-3), Rsamtools(>= 1.21)
Imports data.table, grDevices, clue, cluster, gplots, BiocGenerics(>= 0.31.6), S4Vectors, IRanges, GenomicRanges, Rcpp, TSP, GenomicFiles, gtools, rtracklayer, BiocParallel, DNAcopy, colorspace, reshape2, ggplot2, methods, exomeCopy, GenomicAlignments, diagram
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