contiBAIT: Improves Early Build Genome Assemblies using Strand-Seq Data

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
Date of publication
None
Maintainer
Kieran O'Neill <koneill@bccrc.ca>
License
BSD_2_clause + file LICENSE
Version
1.2.0

View on Bioconductor

Man pages

BAIT
BAIT - master function to process strand-seq libraries into...
barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method
Bar plot all linkage groups, with the true chromosomes of...
ChrTable
A class for storing chromosome/fragment lengths
clusterContigs-StrandStateMatrix-method
clusterContigs - agglomeratively clusters contigs into...
contiBAIT
contiBAIT - master function to process strand-seq libraries...
ContigOrdering
A class for storing contig ordering of a linkage group
exampleChrTable
Example of a ChromosomeTable, containing contigs and their...
exampleContigOrder
Example of a ContigOrdering table, containing a list with a...
exampleCrickFreq
An example Crick strand frequences extracted from BAMS by...
exampleDividedChr
Example of a divided chromosome, containing contigs and their...
exampleLGList
Example of a LinkageGroupList output from clusterContigs
exampleLibList
Example of a LibraryGroupList, containing library names
exampleReadCounts
Example of read counts extracted from BAMS by...
exampleStrandFreq
Example of strand frequencies extracted from BAMS by...
exampleWatsonFreq
An example Watson strand frequences extracted from BAMS by...
exampleWCMatrix
An example StrandStateMatrix containing WW, CC and WC calls...
findSimilarLibraries
findSimilarLibraries - function to identify libraries that...
fixLinkageGroups
fixLinkageGroups - searches for discrepancies within ordered...
highlightAssemblyErrors
highlightAssemblyErrors - Master function to identify...
ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method
ideogramPlot - plots BAIT-like ideograms
LibraryGroupList
A class for storing library group calls for contigs
LinkageGroupList
A class for storing linkage group calls for contigs
locateMisorients
locateMisorients - function to identify libraries that hare...
makeBoxPlot
makeBoxPlot - creates boxplot of contigs included in the...
makeChrTable
makeChrTable - Pulls out chromosome and length data from the...
mapGapFromOverlap
mapGapFromOverlap - function to co-localize strand state...
mergeFlankedLGs
mergeFlankedLGs - searches for similarities at the ends of...
orderAllLinkageGroups
Function to call contig ordering algorithms iteratively...
orderContigsGreedy
Function to order contigs within a single linkage group using...
orderContigsTSP
Attempt to order contigs within linkage groups using...
OrientationFrame
A class for storing contig orientations
plotContigOrder
Plot ordering of contigs within a single linkage group.
plotLGDistances-LinkageGroupList-StrandStateMatrix-method
plotLGDistances - plots a heatmap of the distances between...
plotWCdistribution-StrandFreqMatrix-method
Creates median distribution boxplots across all libraries and...
preprocessStrandTable-StrandFreqMatrix-method
preprocessStrandTable - remove low quality libraries and...
reorientAndMergeLGs
reorientAndMergeLGs uses a simple dissimilarity to find...
show-ContigOrdering-method
show-methods
show-LibraryGroupList-method
show-methods
show-LinkageGroupList-method
show-methods
show-OrientationFrame-method
show-methods
show-StrandFreqMatrix-method
show-methods
show-StrandReadMatrix-method
show-methods
show-StrandStateList-method
show-methods
show-StrandStateMatrix-method
show-methods
StrandFreqMatrix
A class for storing a matrix of frequencies of Watson to...
StrandReadMatrix
A class for storing read counts for a set of contigs over...
strandSeqFreqTable
strandSeqFreqTable - function to process bam files for...
StrandStateList
A class for storing StrandStateList lists for contigs
StrandStateMatrix
A class for storing a data frame of discrete strand states of...
thoroughBed
thoroughBed - function to merge chromosomes from libraries...
writeBed
function to write contig order to BED file

Files in this package

contiBAIT/DESCRIPTION
contiBAIT/LICENSE
contiBAIT/NAMESPACE
contiBAIT/R
contiBAIT/R/AllClasses.R
contiBAIT/R/AllGenerics.R
contiBAIT/R/BAIT.R
contiBAIT/R/barplotLinkageGroupCalls.R
contiBAIT/R/clusterContigs.R
contiBAIT/R/computeConsensus.R
contiBAIT/R/computeSim.R
contiBAIT/R/contiBAIT.R
contiBAIT/R/findSimilarLibraries.R
contiBAIT/R/fixLinkageGroups.R
contiBAIT/R/highlightAssemblyErrors.R
contiBAIT/R/ideogramPlot.R
contiBAIT/R/locateMisorients.R
contiBAIT/R/makeBoxPlot.R
contiBAIT/R/makeChrTable.R
contiBAIT/R/mapGapFromOverlap.R
contiBAIT/R/mergeFlankedLGs.R
contiBAIT/R/orderAllLinkageGroups.R
contiBAIT/R/orderContigsGreedy.R
contiBAIT/R/orderContigsTSP.R
contiBAIT/R/plotContigOrder.R
contiBAIT/R/plotLGDistances.R
contiBAIT/R/plotWCdistribution.R
contiBAIT/R/preprocessStrandTable.R
contiBAIT/R/reorientAndMergeLGs.R
contiBAIT/R/strandSeqFreqTable.R
contiBAIT/R/thoroughBed.R
contiBAIT/R/writeBed.R
contiBAIT/README.md
contiBAIT/build
contiBAIT/build/vignette.rds
contiBAIT/data
contiBAIT/data/exampleChrTable.rda
contiBAIT/data/exampleContigOrder.rda
contiBAIT/data/exampleCrickFreq.rda
contiBAIT/data/exampleDividedChr.rda
contiBAIT/data/exampleLGList.rda
contiBAIT/data/exampleLibList.rda
contiBAIT/data/exampleReadCounts.rda
contiBAIT/data/exampleStrandFreq.rda
contiBAIT/data/exampleWCMatrix.rda
contiBAIT/data/exampleWatsonFreq.rda
contiBAIT/inst
contiBAIT/inst/NEWS
contiBAIT/inst/doc
contiBAIT/inst/doc/contiBAIT.R
contiBAIT/inst/doc/contiBAIT.Rnw
contiBAIT/inst/doc/contiBAIT.pdf
contiBAIT/inst/examples
contiBAIT/inst/examples/BAIT.R
contiBAIT/inst/examples/barplotLinkageGroupCalls.R
contiBAIT/inst/examples/clusterContigs.R
contiBAIT/inst/examples/contiBAIT.R
contiBAIT/inst/examples/findSimilarLibraries.R
contiBAIT/inst/examples/ideogramPlot.R
contiBAIT/inst/examples/makeBoxPlot.R
contiBAIT/inst/examples/makeChrTable.R
contiBAIT/inst/examples/mapGapFromOverlap.R
contiBAIT/inst/examples/orderAllLinkageGroups.R
contiBAIT/inst/examples/plotContigOrder.R
contiBAIT/inst/examples/plotLGDistances.R
contiBAIT/inst/examples/plotWCdistribution.R
contiBAIT/inst/examples/preprocessStrandTable.R
contiBAIT/inst/examples/reorientAndMergeLGs.R
contiBAIT/inst/examples/strandSeqFreqTable.R
contiBAIT/inst/examples/thoroughBed.R
contiBAIT/inst/examples/writeBed.R
contiBAIT/inst/extdata
contiBAIT/inst/extdata/StrandSeqTestData_1.bam
contiBAIT/inst/extdata/StrandSeqTestData_10.bam
contiBAIT/inst/extdata/StrandSeqTestData_11.bam
contiBAIT/inst/extdata/StrandSeqTestData_12.bam
contiBAIT/inst/extdata/StrandSeqTestData_13.bam
contiBAIT/inst/extdata/StrandSeqTestData_14.bam
contiBAIT/inst/extdata/StrandSeqTestData_15.bam
contiBAIT/inst/extdata/StrandSeqTestData_16.bam
contiBAIT/inst/extdata/StrandSeqTestData_17.bam
contiBAIT/inst/extdata/StrandSeqTestData_18.bam
contiBAIT/inst/extdata/StrandSeqTestData_19.bam
contiBAIT/inst/extdata/StrandSeqTestData_2.bam
contiBAIT/inst/extdata/StrandSeqTestData_20.bam
contiBAIT/inst/extdata/StrandSeqTestData_21.bam
contiBAIT/inst/extdata/StrandSeqTestData_22.bam
contiBAIT/inst/extdata/StrandSeqTestData_23.bam
contiBAIT/inst/extdata/StrandSeqTestData_24.bam
contiBAIT/inst/extdata/StrandSeqTestData_25.bam
contiBAIT/inst/extdata/StrandSeqTestData_26.bam
contiBAIT/inst/extdata/StrandSeqTestData_27.bam
contiBAIT/inst/extdata/StrandSeqTestData_28.bam
contiBAIT/inst/extdata/StrandSeqTestData_29.bam
contiBAIT/inst/extdata/StrandSeqTestData_3.bam
contiBAIT/inst/extdata/StrandSeqTestData_30.bam
contiBAIT/inst/extdata/StrandSeqTestData_31.bam
contiBAIT/inst/extdata/StrandSeqTestData_32.bam
contiBAIT/inst/extdata/StrandSeqTestData_33.bam
contiBAIT/inst/extdata/StrandSeqTestData_34.bam
contiBAIT/inst/extdata/StrandSeqTestData_35.bam
contiBAIT/inst/extdata/StrandSeqTestData_4.bam
contiBAIT/inst/extdata/StrandSeqTestData_5.bam
contiBAIT/inst/extdata/StrandSeqTestData_6.bam
contiBAIT/inst/extdata/StrandSeqTestData_7.bam
contiBAIT/inst/extdata/StrandSeqTestData_8.bam
contiBAIT/inst/extdata/StrandSeqTestData_9.bam
contiBAIT/man
contiBAIT/man/BAIT.Rd
contiBAIT/man/ChrTable.Rd
contiBAIT/man/ContigOrdering.Rd
contiBAIT/man/LibraryGroupList.Rd
contiBAIT/man/LinkageGroupList.Rd
contiBAIT/man/OrientationFrame.Rd
contiBAIT/man/StrandFreqMatrix.Rd
contiBAIT/man/StrandReadMatrix.Rd
contiBAIT/man/StrandStateList.Rd
contiBAIT/man/StrandStateMatrix.Rd
contiBAIT/man/barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method.Rd
contiBAIT/man/clusterContigs-StrandStateMatrix-method.Rd
contiBAIT/man/contiBAIT.Rd
contiBAIT/man/exampleChrTable.Rd
contiBAIT/man/exampleContigOrder.Rd
contiBAIT/man/exampleCrickFreq.Rd
contiBAIT/man/exampleDividedChr.Rd
contiBAIT/man/exampleLGList.Rd
contiBAIT/man/exampleLibList.Rd
contiBAIT/man/exampleReadCounts.Rd
contiBAIT/man/exampleStrandFreq.Rd
contiBAIT/man/exampleWCMatrix.Rd
contiBAIT/man/exampleWatsonFreq.Rd
contiBAIT/man/findSimilarLibraries.Rd
contiBAIT/man/fixLinkageGroups.Rd
contiBAIT/man/highlightAssemblyErrors.Rd
contiBAIT/man/ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method.Rd
contiBAIT/man/locateMisorients.Rd
contiBAIT/man/makeBoxPlot.Rd
contiBAIT/man/makeChrTable.Rd
contiBAIT/man/mapGapFromOverlap.Rd
contiBAIT/man/mergeFlankedLGs.Rd
contiBAIT/man/orderAllLinkageGroups.Rd
contiBAIT/man/orderContigsGreedy.Rd
contiBAIT/man/orderContigsTSP.Rd
contiBAIT/man/plotContigOrder.Rd
contiBAIT/man/plotLGDistances-LinkageGroupList-StrandStateMatrix-method.Rd
contiBAIT/man/plotWCdistribution-StrandFreqMatrix-method.Rd
contiBAIT/man/preprocessStrandTable-StrandFreqMatrix-method.Rd
contiBAIT/man/reorientAndMergeLGs.Rd
contiBAIT/man/show-ContigOrdering-method.Rd
contiBAIT/man/show-LibraryGroupList-method.Rd
contiBAIT/man/show-LinkageGroupList-method.Rd
contiBAIT/man/show-OrientationFrame-method.Rd
contiBAIT/man/show-StrandFreqMatrix-method.Rd
contiBAIT/man/show-StrandReadMatrix-method.Rd
contiBAIT/man/show-StrandStateList-method.Rd
contiBAIT/man/show-StrandStateMatrix-method.Rd
contiBAIT/man/strandSeqFreqTable.Rd
contiBAIT/man/thoroughBed.Rd
contiBAIT/man/writeBed.Rd
contiBAIT/src
contiBAIT/src/Makevars
contiBAIT/src/Makevars.win
contiBAIT/src/computeSim.cpp
contiBAIT/src/computeSim.h
contiBAIT/src/orderContigsGreedy.cpp
contiBAIT/src/orderContigsGreedy.h
contiBAIT/vignettes
contiBAIT/vignettes/contiBAIT.Rnw