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contiBAIT (version 1.0.0)

Improves Early Build Genome Assemblies using Strand-Seq Data

Description

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.

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Version

Version

1.0.0

License

BSD_2_clause + file LICENSE

Maintainer

Kieran ONeill

Last Published

February 15th, 2017

Functions in contiBAIT (1.0.0)

StrandStateMatrix-class

A class for storing a data frame of discrete strand states of a set of contigs over several libraries

BAIT -- master function to process strand-seq libraries into BAIT ideograms

show,ContigOrdering-method

plotLGDistances,LinkageGroupList,StrandStateMatrix-method

plotLGDistances -- plots a heatmap of the distances between linkage groups

orderAllLinkageGroups,LinkageGroupList,StrandStateMatrix,StrandFreqMatrix,StrandReadMatrix-method

Function to call contig ordering algorithms iteratively across each linkage group element

exampleCrickFreq

An example Crick strand frequences extracted from BAMS by strandSeqFreqTable where BAITtables=TRUE

contiBAIT -- master function to process strand-seq libraries into ordered linkage groups

preprocessStrandTable,StrandFreqMatrix-method

preprocessStrandTable -- remove low quality libraries and contigs before attempting to build a genome

show,StrandFreqMatrix-method

exampleReadCounts

Example of read counts extracted from BAMS by strandSeqFreqTable

show,OrientationFrame-method

writeBed,ANY,OrientationFrame,ContigOrdering-method

function to write contig order to BED file

barplotLinkageGroupCalls,LinkageGroupList,ChrTable-method

Bar plot all linkage groups, with the true chromosomes of contigs coloured.

exampleStrandFreq

Example of strand frequencies extracted from BAMS by strandSeqFreqTable

mapGapFromOverlap

mapGapFromOverlap -- function to co-localize strand state changes with assembly gaps

makeChrTable -- Pulls out chromosome and length data from the header of a bam file

exampleWCMatrix

An example StrandStateMatrix containing WW, CC and WC calls for contigs

makeBoxPlot,ChrTable,LinkageGroupList-method

makeBoxPlot -- creates boxplot of contigs included in the analysis vs those excluded

A class for storing chromosome/fragment lengths

plotContigOrder

Plot ordering of contigs within a single linkage group.

show,StrandStateMatrix-method

OrientationFrame-class

A class for storing contig orientations

orderContigsTSP

Attempt to order contigs within linkage groups using travelling salesperson algorithm

Example of a LinkageGroupList output from clusterContigs

mergeLinkageGroups,LinkageGroupList,StrandStateMatrix-method

mergeLinkageGroups -- merge very similar linkage groups, including those in reverse orientation

StrandFreqMatrix-class

A class for storing a matrix of frequencies of Watson to Crick reads for a set of contigs over several libraries

exampleChrTable

Example of a ChromosomeTable, containing contigs and their lengths

show,LinkageGroupList-method

plotWCdistribution,StrandFreqMatrix-method

Creates median distribution boxplots across all libraries and contigs

strandSeqFreqTable

strandSeqFreqTable -- function to process bam files for contiBAIT

ideogramPlot,StrandReadMatrix,StrandReadMatrix,ChrTable-method

ideogramPlot -- plots BAIT-like ideograms

ContigOrdering-class

A class for storing contig ordering of a linkage group

show,StrandReadMatrix-method

exampleDividedChr

Example of a divided chromosome, containing contigs and their lengths

orderContigsGreedy

Function to order contigs within a single linkage group using a greedy algorithms Attempt to order contigs within

LinkageGroupList-class

A class for storing linkage group calls for contigs

reorientLinkageGroups,LinkageGroupList,StrandStateMatrix-method

reorientLinkageGroups uses a simple dissimilarity to find misoriented fragments within linkage groups.

StrandReadMatrix-class

A class for storing read counts for a set of contigs over several libraries

exampleWatsonFreq

An example Watson strand frequences extracted from BAMS by strandSeqFreqTable where BAITtables=TRUE

clusterContigs,StrandStateMatrix-method

clusterContigs -- agglomeratively clusters contigs into linkage groups based on strand inheritance