interOpsReport: Function to parse InterOps files and generate summary reports

In ThomasCarroll/basecallQC: Working with Illumina Basecalling and Demultiplexing input and output files

Description

Parses the InterOps binary files produced by Illumina's Real Time Analysis sofware and used by Illumina's SAV sofware. InterOp binary files contain information on phasing/prephsing, yield,read numbers and basecalling quality score distributions per cycle. This interOpsReport functions parses and summarises the InterOps files, TileMetrics.bin and QMetrics.bin, and the Stats directory XML files, ConversionStats.xml and DemultiplexingStats.xml.

Usage

interOpsReport(bcl2fastqparams, verbose = TRUE)

Arguments

bcl2fastqparams	A BCL2FastQparams object.
verbose	TRUE or FALSE . TRUE reports progress through file parsing.

Details

The interOpsReport function returns a list of machine and run information, basecalling quality information and demultiplexing information. The three named elements are descibed below.

• "machineReport" A data.frame containing information machine and software parameters

• "sequencingReport" A data.frame of mean cluster density, percentage clusters passing filter, phasing and prephasing percentages, number of reads total/passing filter and percent of reads with mean quality score > Q30 grouped by lane and read

• "demuxReport" A data.frame of demultiplexing results containing yield, number of reads, percentage of reads with quality scores greater than >Q30 and the percent of total reads per lane. Results are summarised per lane for samples, underdetermined indexes and all indexes (identifed and unidentified).

Value

A named list of length 3 containing machine and run information, basecalling quality information and demultiplexing information.

Author(s)

Thomas Carroll.

Examples

fileLocations <- system.file("extdata",package="basecallQC")
runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE)
config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE)

# myRes_BCAGJ8ANXX <- interOpsReport(bcl2fastqparams,verbose=TRUE) 

ThomasCarroll/basecallQC documentation built on May 9, 2019, 4:45 p.m.