seqTools-package: SeqTools: Bioconductor package for analysis of FASTQ and...

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 <kaisers@med.uni-duesseldorf.de>

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 Nov. 8, 2020, 5:20 p.m.