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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("contiBAIT")
AuthorKieran O'Neill, Mark Hills, Mike Gottlieb
Bioconductor views CellBasedAssays Genetics GenomeAssembly QualityControl WholeGenome
Date of publicationNone
MaintainerKieran O'Neill <koneill@bccrc.ca>
LicenseBSD_2_clause + file LICENSE
Version1.2.0

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

Functions

BAIT Man page
barplotLinkageGroupCalls Man page
barplotLinkageGroupCalls,LinkageGroupList,ChrTable-method Man page
barplotLinkageGroupCalls,LinkageGroupList,LinkageGroupList-metho Man page
ChrTable Man page
ChrTable-class Man page
clusterContigs Man page
clusterContigs,StrandStateMatrix-method Man page
clusterContigs,StrandStateMatrix,StrandStateMatrix-method Man page
contiBAIT Man page
ContigOrdering Man page
ContigOrdering-class Man page
exampleChrTable Man page
exampleContigOrder Man page
exampleCrickFreq Man page
exampleDividedChr Man page
exampleLGList Man page
exampleLibList Man page
exampleReadCounts Man page
exampleStrandFreq Man page
exampleWatsonFreq Man page
exampleWCMatrix Man page
findSimilarLibraries Man page
findSimilarLibraries,findSimilarLibraries-StrandStateMatrix-Stra Man page
findSimilarLibraries,StrandStateMatrix,StrandReadMatrix,ChrTable Man page
fixLinkageGroups Man page
fixLinkageGroups,ContigOrdering,StrandStateList,LinkageGroupList Man page
fixLinkageGroups-ContigOrdering-StrandStateList-method Man page
highlightAssemblyErrors Man page
highlightAssemblyErrors,highlightAssemblyErrors-GRanges-method Man page
ideogramPlot Man page
ideogramPlot,StrandReadMatrix,StrandReadMatrix,ChrTable-method Man page
ideogramPlot,StrandReadMatrix,StrandReadMatrix-method,ChrTable,C Man page
LibraryGroupList Man page
LibraryGroupList-class Man page
LinkageGroupList Man page
LinkageGroupList-class Man page
locateMisorients Man page
locateMisorients,GRanges-method Man page
locateMisorients,locateMisorients-GRanges-method Man page
makeBoxPlot Man page
makeBoxPlot-ChrTable-LinkageGroupList-method Man page
makeBoxPlot,ChrTable,LinkageGroupList-method Man page
makeChrTable Man page
mapGapFromOverlap Man page
mergeFlankedLGs Man page
mergeFlankedLGs,LinkageGroupList,StrandStateMatrix-method Man page
orderAllLinkageGroups Man page
orderAllLinkageGroups,LinkageGroupList,StrandStateMatrix,StrandF Man page
orderAllLinkageGroups,orderAllLinkageGroups-LinkageGroupList-Str Man page
orderContigsGreedy Man page
orderContigsTSP Man page
OrientationFrame Man page
OrientationFrame-class Man page
plotContigOrder Man page
plotContigOrder,ContigOrdering-method Man page
plotLGDistances Man page
plotLGDistances,LinkageGroupList,LinkageGroupList-method Man page
plotLGDistances,LinkageGroupList,StrandStateMatrix-method Man page
plotWCdistribution Man page
plotWCdistribution,StrandFreqMatrix-method Man page
plotWCdistribution,StrandFreqMatrix,StrandFreqMatrix-method Man page
preprocessStrandTable Man page
preprocessStrandTable,StrandFreqMatrix-method Man page
preprocessStrandTable,StrandFreqMatrix,StrandFreqMatrix-method Man page
reorientAndMergeLGs Man page
reorientAndMergeLGs-LinkageGroupList-StrandStateMatrix-method Man page
reorientAndMergeLGs,LinkageGroupList,StrandStateMatrix-method Man page
show,ContigOrdering-method Man page
show,LibraryGroupList-method Man page
show,LinkageGroupList-method Man page
show,OrientationFrame-method Man page
show,StrandFreqMatrix-method Man page
show,StrandReadMatrix-method Man page
show,StrandStateList-method Man page
show,StrandStateMatrix-method Man page
StrandFreqMatrix Man page
StrandFreqMatrix-class Man page
StrandReadMatrix Man page
StrandReadMatrix-class Man page
strandSeqFreqTable Man page
StrandStateList Man page
StrandStateList-class Man page
StrandStateMatrix Man page
StrandStateMatrix-class Man page
thoroughBed Man page
thoroughBed,ANY,LibraryGroupList-method Man page
thoroughBed,thoroughBed-LibraryGroupList-method Man page
writeBed Man page
writeBed,ANY,OrientationFrame,ContigOrdering-method Man page
writeBed-OrientationFrame-ContigOrdering-method Man page

Files

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

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