seqTools-package: Analysis of fastq and fasta files.

Description Details Author(s) References Examples

Description

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

Details

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

Author(s)

Wolfgang Kaisers

Maintainer: Wolfgang Kaisers <[email protected]>

References

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

Examples

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# 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)

seqTools documentation built on May 31, 2017, 1:59 a.m.