Search Results for "phred"

ArtificialFastqGenerator takes the reference genome (in FASTA format) as input and outputs artificial FASTQ files in the Sanger format. It can accept Phred base quality scores from existing FASTQ files, and use them to simulate sequencing errors. Since the artificial FASTQs are derived from the reference genome, the reference genome provides a gold-standard for calling variants (Single Nucleotide Polymorphisms (SNPs) and insertions and deletions (indels)). This enables evaluation of a Next Generation Sequencing (NGS) analysis pipeline which aligns reads to the reference genome and then calls the variants.

...It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously. It works for both of single-end and paired-end reads.Specificity and sensitivity has been validate by Illumina IM SNP array. In default threshold (Phred scale score > 20), it could detect 92.21% heterozygous SNPs with 0.14% false positive rate (90.88% sensitivity in C/T SNPs with 0.16% false positive rate, 98.51% sensitivity in non C/T SNPs with 0.16% false positive rate). Cytosine calling is not only based on reference context, so it could detect non-reference cytosine context.

A perl script that converts Illumina qseq files into Phred fastq files for use in Maq. Originally written by Tyler Bachman from UC Riverside, adapted by Eugene Goltsman. Freely available under the terms of GNU GPLv3.