seqTools (version 1.6.0)

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

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

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

# 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)