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R453Plus1Toolbox (version 1.22.0)

A package for importing and analyzing data from Roche's Genome Sequencer System

Description

The R453Plus1 Toolbox comprises useful functions for the analysis of data generated by Roche's 454 sequencing platform. It adds functions for quality assurance as well as for annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. Further, a pipeline for the detection of structural variants is provided.

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Version

Version

1.22.0

License

LGPL-3

Maintainer

HansUlrich Klein

Last Published

February 15th, 2017

Functions in R453Plus1Toolbox (1.22.0)

baseQualityStats

Statistics Of Base Quality

dinucleotideOddsRatio

Dinucleotide Odds Ratio

Plots variant positions

Amplicon Variant Analyzer data import

coverageOnTarget

Computes the coverage restricted to the target region.

getAlignedReads

Import reads from an Amplicon Variant Analyzer project

Absolute And Relative Frequency Of The Four Bases.

nucleotideCharts

Nucleotide Charts

Access the amplicon data of an AVASet

homopolymerHist

Create A Histogram Of The Homopolymer Stretches

Class "SFFRead"

sequenceQualityHist

A Histogram Of The Sequence Qualities

HTML-Report Builder for the AVASet and MapperSet

Example data for plotVariants

SFFContainer-class

Class "SFFContainer"

Custom capture array design

Remove linker sequences located at the start of short reads

mergeBreakpoints

Identify and merge related breakpoints caused by the same variant.

Basic functions for CIGAR strings

positionQualityBoxplot

Boxplot Of The Quality For Each Position

Calculate The Overall GC-Content

Example data for plotVariants

Access the amplicon data of an AVASet.

Class to contain Amplicon Variant Analyzer Output

setVariantFilter

Filters output of variant information

Putative breakpoints of chimeric reads

Get amino acid abbreviations

filterChimericReads

Extract chimeric reads and apply filtering steps to remove artificial chimeric reads.

alignShortReads

Exact alignment of DNA sequences against a reference

Example data for plotVariants

Creating a MapperSet

Check for each read whether it aligns within the given region.

plotVariationFrequency

Create an AVA style variation frequency plot

Function To Write Files In Roche's .sff Format

Histogram Of The Read Lengths

Write A SFFContainer Object To A FASTQ File

sequenceCaptureLinkers

Retrieve NimbleGen's sequence capture linkers

MapperSet-class

Class to Contain GS Reference Mapper Output

Breakpoints-class

Class "Breakpoints"

baseQualityHist

Plot A Histogram Of The Base Qualities.

avaSetFiltered_annot

AVASet variant annotations

complexity.dust

Sequence Complexity Using The DUST Algorithm

AnnotatedVariants-class

Class "AnnotatedVariants"

complexity.entropy

Sequence Complexity Using The Shannon-Wiener Algorithm

Amplicon Variant Analyzer data import

getVariantPercentages

Variant coverage

annotateVariants

Adds genomic information to variants

mapperSetExample

GS Reference Mapper data import

genomeSequencerMIDs

Retrieve GS multiplex sequences

Function To Read In Roche's .sff Files

detectBreakpoints

Clustering and consensus breakpoint detection for chimeric reads

GC-Content Histogram

plotAmpliconCoverage

Creates a plot visualizing the number of reads per amplicon

referenceSequences

Access the reference sequences of an AVASet

flowgramBarplot

Create A Barplot Of The Flow Intensities

GC-Content Per Position

Convert an AVASet object into a VCF object

Access the amplicon data of an AVASet.

demultiplexReads

Performs MID/Multiplex filtering

Creating an AVASet

Calculate transition transversion ratio

plotChimericReads

Plots chimeric reads

qualityReportSFF

Function To Create A Quality Report In PDF Format

readLengthStats

Statistics For The Read Lengths