README.md

In csf-ngs/illuminasavr: Parse and Plot illumina SAV interop binary metric files

illuminasavr

R functions for parsing of Illumina SAV (sequence analysis viewer) files, plotting with ggplot2 and generation of a website.

The website allows you to interactively explore the data (see screenshot).

Uses: R, angular.js, d3.js

install

library("devtools")
install_github("illuminasavr", "csf-ngs")
library("illuminasavr")

#generate web-site in outputfolder
makeSite("/full/path/to/InterOp", "/full/path/to/outputfolder")

#generate web-site in runfolder
makeSiteInRunfolder("/full/path/to/Runfolder")

screenshot:

TODO

• switch binary parsing backend to https://github.com/Illumina/interop
• [] make Q30,Q20 mean/median/truncated mean identical to illuminas (don't really know what illumina uses).
• [] table of data
• [] add request to server for sample info metadata
• [] don't load everything multiple times in the controller

REMARK:

• The website now also soft links the Thumbnails_Images folder into the generated folder to be able to view the images.

• Currently it parses QMetricsOut.bin version 5 files RTA 1.18.64+ There is a parser for QMetricsOut.bin version 4 in the source code. In parser.R just change

R qmet <- parseFile(qmet, qualityMetricsParser5(), FALSE) qmet <- qualityMetricsParser5()$toStats(qmet) //to qmet <- parseFile(qmet, qualityMetricsParser4(), FALSE) qmet <- qualityMetricsParser4()$toStats(qmet) - MiSeq is not supported - NextSeq is not supported - NovaSeq is not supported

If there is time in the future, the backend parsing will be done by https://github.com/Illumina/interop and this package will only create a website with the data

csf-ngs/illuminasavr documentation built on May 14, 2019, 12:11 p.m.