Quality Control Tool for High-Throughput Sequencing Data

Description

Rqc is an optimized tool designed for quality assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces a report, which contains a set of high-resolution images that can be directly used on publications.

Author(s)

Welliton Souza, Benilton Carvalho

Maintainer: Welliton Souza <well309@gmail.com>

Examples

  options(device.ask.default = FALSE)
  folder <- system.file(package="ShortRead", "extdata/E-MTAB-1147")
  rqc(folder, ".fastq.gz", pair=c(1,1), workers=1)
  

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Rqc)
Loading required package: BiocParallel
Loading required package: ShortRead
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Rqc/Rqc-package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Rqc-package
> ### Title: Quality Control Tool for High-Throughput Sequencing Data
> ### Aliases: Rqc Rqc-package
> ### Keywords: package
> 
> ### ** Examples
> 
> 
>   options(device.ask.default = FALSE)
>   folder <- system.file(package="ShortRead", "extdata/E-MTAB-1147")
>   rqc(folder, ".fastq.gz", pair=c(1,1), workers=1)
'/tmp/RtmpXqOWYs/rqc_report.html' has been created.
Warning message:
closing unused connection 3 (/home/ddbj/local/lib64/R/library/ShortRead/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz) 
>   
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>