Package: basecallQC 1.31.0
Thomas Carroll
basecallQC: Working with Illumina Basecalling and Demultiplexing input and output files
The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.
Authors:
basecallQC_1.31.0.tar.gz
basecallQC_1.31.0.zip(r-4.5)basecallQC_1.31.0.zip(r-4.4)basecallQC_1.31.0.zip(r-4.3)
basecallQC_1.31.0.tgz(r-4.4-any)basecallQC_1.31.0.tgz(r-4.3-any)
basecallQC_1.31.0.tar.gz(r-4.5-noble)basecallQC_1.31.0.tar.gz(r-4.4-noble)
basecallQC_1.31.0.tgz(r-4.4-emscripten)basecallQC_1.31.0.tgz(r-4.3-emscripten)
basecallQC.pdf |basecallQC.html✨
basecallQC/json (API)
NEWS
| # Install 'basecallQC' in R: |
| install.packages('basecallQC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:basecallQC-1.29.0(bioc 3.20)basecallQC-1.28.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
sequencinginfrastructuredataimportqualitycontrol
Last updated 23 days agofrom:0ca2dc6b92. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 30 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 30 2024 |
| R-4.4-mac | NOTE | Oct 30 2024 |
| R-4.3-win | OK | Oct 30 2024 |
| R-4.3-mac | OK | Oct 30 2024 |
Exports:baseCallMetricsbasecallQCBCL2FastQparamscreateBasemaskscreateBCLcommanddemultiplexMetricsdemuxBarplotdemuxBoxplotindexlengthsindexlengths.bcl2fastqparamsinterOpsReportmakeFQTablepassFilterBarpassFilterBoxplotpassFilterTilePlotreadlengthsreadlengths.bcl2fastqparamsreportBCLsummaryConvStatsTablesummaryDemuxTablevalidateBCLSheet
Dependencies:abindaskpassbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitopsbslibcachemclicodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDelayedArraydeldirdigestdplyrDTevaluatefansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttpuvhttrhwriterinterpIRangesisobandjpegjquerylibjsonliteknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigpngprettydocpromisespurrrpwalignR6rappdirsrasterRColorBrewerRcppRcppEigenRhtslibrlangrmarkdownRsamtoolsS4ArraysS4VectorssassscalesShortReadsnowspSparseArraystringistringrSummarizedExperimentsysterratibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Gather basecalling metrics from a Run (using Run's ConversionStats.xml file). | baseCallMetrics |
| The basecallQC object and constructor. | basecallQC basecallQC-basecallQC basecallQC-class |
| The Parameters for BCL2FastQparams object. | BCL2FastQparams BCL2FastQparams-BCL2FastQparams BCL2FastQparams-class |
| Function to create basemasks for basecalling from Illumina samplesheet (for bcl2Fastq versions >= 2.1.7). | createBasemasks |
| Function to create command for Illumina basecalling/demultiplexing using bcl2fastq versions >= 2.1.7. | createBCLcommand |
| Gather demultiplexing metrics from a Run (using Run's DemultiplexingStats.xml file). | demultiplexMetrics |
| Barplot of Illumina demultiplexing statistics. | demuxBarplot demuxBarplot,baseCallQC-method demuxBarplot,basecallQC-method demuxBarplot,list-method demuxBarplot.basecallQC |
| Boxplot of Illumina demultiplexing statistics. | demuxBoxplot demuxBoxplot,baseCallQC-method demuxBoxplot,basecallQC-method demuxBoxplot,list-method demuxBoxplot.basecallQC |
| Index lengths | indexlengths indexlengths,BCL2FastQparams-method indexlengths,BCL2FastQparams-method, indexlengths.bcl2fastqparams |
| Function to parse InterOps files and generate summary reports | interOpsReport |
| Generate an HTML table linking to per sample summary fastq QC statistics from ShortRead | makeFQTable |
| Barplot of Illumina basecalling statistics for reads passing filter. | passFilterBar passFilterBar,baseCallQC-method passFilterBar,basecallQC-method passFilterBar,list-method passFilterBar.basecallQC |
| Boxplot of Illumina basecalling statistics for reads passing filter. | passFilterBoxplot passFilterBoxplot,baseCallQC-method passFilterBoxplot,basecallQC-method passFilterBoxplot,list-method passFilterBoxplot.basecallQC |
| Tile plot of Illumina basecalling statistics for reads passing filter. | passFilterTilePlot passFilterTilePlot,baseCallQC-method passFilterTilePlot,basecallQC-method passFilterTilePlot,list-method passFilterTilePlot.basecallQC |
| Read lengths | readlengths readlengths,BCL2FastQparams-method readlengths,BCL2FastQparams-method, readlengths.bcl2fastqparams |
| Generate basecallQC report | reportBCL reportBCL,baseCallQC-method reportBCL,basecallQC-method reportBCL.basecallQC |
| Creates an HTML table of per sample summary statistics from basecalling results | summaryConvStatsTable summaryConvStatsTable,baseCallQC-method summaryConvStatsTable,basecallQC-method summaryConvStatsTable,list-method summaryConvStatsTable.basecallQC |
| Generate an HTML table of per sample summary demultiplexing statistics | summaryDemuxTable summaryDemuxTable,baseCallQC-method summaryDemuxTable,basecallQC-method summaryDemuxTable,list-method summaryDemuxTable.basecallQC |
| Illumina sample sheet cleaning and updating for bcl2Fastq versions >= 2.1.7 | validateBCLSheet |
