writeSimContFastq: writeSimContFastq: Create FASTQ files with simulated k-mer...

In wokai/seqTools: Analysis of nucleotide, sequence and quality content on fastq files.

Description

Writes compressed FASTQ files where sequence sections contain concatenated k-mers which are uniformly distributed in the range of k-mers for given k. A fraction of the reads can be contaminated with one or more deterministic k-mers.

Usage

 writeSimContFastq(k=6, nk=5, nSeq=10, pos=1,
        kIndex=1, nContam=nSeq, filename="simc.fq.gz")

Arguments

k	numeric. Length of k-mer. Default value is 6.

nk	numeric. Number of k-mers in each FASTQ read. Default value is 5.

nSeq	numeric. Number of simulated reads in FASTQ-file. Default value is 10.

pos	numeric. Determines at which position in sequence the k-mer is inserted. 1-based (1=first position).

kIndex

numeric. k-mer index of inserted k-mer. The k-mer index can be retreaved for a given k-mer with 'kMerIndex'.

nContam

numeric. Absolute number of contaminated reads. The k-mer's are inserted at the firsts 'nContam' reads of the sequence array.

filename

character. Name of written (compressed) FASTQ file.

Details

The read headers are consequtive numbered. The phred quality values are equally set to 46 (='.') which represents a phred value of 13. This function is not designed for routine use. The random content FASTQ files can be used in order to measure the separation capabilities of hierarchical clustering mechanisms.

Value

None.

Author(s)

Wolfgang Kaisers

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

## Not run: writeSimContFastq()

wokai/seqTools documentation built on May 4, 2019, 9:46 a.m.