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seqTools (version 1.6.0)

Analysis of nucleotide, sequence and quality content on fastq files.

Description

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

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Version

Version

1.6.0

License

Artistic-2.0

Maintainer

Wolfgang Kaisers

Last Published

February 15th, 2017

Functions in seqTools (1.6.0)

seqTools-package

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

Class "Fastqq"
phredDist

phredDist: Global relative content of Phred values in Fastqq objects (or subsets).
countDnaKmers

countDnaKmers: Counting k-mers in DNA sequence.
ascii2char

ascii2char: Converting ASCII encoded values to character values.
meltDownK

meltDownK: Condensing DNA k-mer count data to lower k-value (i.e. shorter DNA motifs).
plotKmerCount

plotKmerCount: Creation of plots DNA for k-mer counts from Fastqq objects.
plotNucFreq

plotNucFreq: Plots the position wise relative nucleotide content for nucleotides 'A','C','G','T'.
mergedPhred

mergedPhred functions: Retrieving and plotting of phred quantities from whole Fastqq objects.
simFastqqRunTimes

simFastqqRunTimes: For given values of k and nSeq the function creates FASTQ files with simulated data, collects k-mer data with the fastqq function and reports the run times for the data collection.
kMerIndex

kMerIndex function: Returns array index for given DNA k-mers.
collectDur

collectDur: Returning elapsed time (in seconds) for collection of data from FASTQ files.
cbDistMatrix

cbDistMatrix function: Calculates pairwise distance matrix from DNA k-mer counts based on a modified Canberra distance.
gcContentMatrix

gcContentMatrix: Returns matrix with read counts for GC content.
plotGCcontent

plotGCcontent: Plots the proportions of relative GC content for all FASTQ files.
countSpliceKmers

countSpliceKmers: Counting K-mers on donor (5', upstream) sides (exonic) of splice sites.
plotPhredQuant

plotPhredQuant: Plots the position wise 10%, 25 %, 50%, 75% and 90 % quantiles of phred values.
fastqKmerLocs

fastqKmerLocs function: Counts DNA k-mers position wise from FASTQ files.
phredTable

phredTable: Returns a data.frame with phred encodings.
writeSimFastq

writeSimFastq: Create FASTQ files with simulated DNA k-mer sequences
propPhred

propPhred: Lane specific proportion of reads in a specified Phred-region.
plotNucCount

plotNucCount: Plots nucleotide counts from Fastqq objects.
revCountDnaKmers

revCountDnaKmers: Counting K-mers in DNA sequence.
countGenomeKmers

countGenomeKmers: Counting K-mers in DNA sequences.
writeSimContFastq

writeSimContFastq: Create FASTQ files with simulated k-mer sequences
fastqKmerSubsetLocs

fastqKmerSubsetLocs function: Counts for a given DNA k-mer subset position wise from FASTQ files.
mergeFastqq

mergeFastqq: Merges two Fastqq object into one.
trimFastq

trimFastq: Performs sequence removal, trimming (fixed and quality based) and nucleotide masking on FASTQ files.
writeFai

writeFai: Create FASTA index file.
sim_fq

sim_fq: Performs an experimental series of separation capabilities of hierarchical clustering (HC) based on DNA k-mers in FASTQ files using simulated DNA content.
countFastaKmers

countFastaKmers function: Counts DNA k-mers from (compressed) fasta files.
fastqq

fastqq function: Reading summarizing information from FASTQ files.