seqTools-package: Analysis of fastq and fasta files.
In seqTools: Analysis of nucleotide, sequence and quality content on fastq files.

Description Details Author(s) References Examples

Analyze read length, phred scores and alphabeth frequency and DNA k-mers on uncompressed and compressed files.

Package:	seqTools
Type:	Package
Version:	0.99.31
Date:	2013-10-14
License:	GPL-2
Depends:	methods

Wolfgang Kaisers

Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>

Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM The sanger fastq file format for sequences with quality scores and the Solexa/Illumina fastq variants. Nucleic Acids Research 2010 Vol.38 No.6 1767-1771

# A) Count DNA k-mer
countDnaKmers("ATAAATA",2)
# B) Quality check on fastq file
basedir<-system.file("extdata",package="seqTools")
setwd(basedir)
fq<-fastqq("test_l6.fq")
plotPhredQuant(fq,1)