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Sequence applications

Purpose of these web pages

This set of web pages contain the sequence analysis programs and are split into two groups.

Quality control

This section contains quality control programs which detect and reject low quality sequence data.

  • ABI_QC screens AB1 files for the signal to noise ratio calculated by the ABI base calling software.
  • MaximumPhred calculates the maximum Phred score for a given length of sequence for each Phred (*.phd.1) file in a folder. This data is compared to a user defined cut off and the result is saved to a file.
  • RegionOfInterest is similar to MaximumPhred except the user supplies a sequence and the program calculates the average Phred score across this region in each Phred (*.phd.1) file.
  • dbQC is an extension of MaximumPhred, storing the quality score data in an access database which can then be queried to find trends and there possible cause in sequence quality.
Sequence analysis

Currently this section contains:

  • CpGViewer which aids analysis of bisulphite treated DNA sequences.
  • Genescreen is a sequence variant detection and annotation program.
  • gSNP is similar to QSVanalyser but genotypes SNPs in trace files.
  • Illuminator is a program that analyses data from an Illumina clonal sequencer, however unlike many clonal sequencing programs it is designed to screen one gene in many people, rather than many genes in one person.
    • FindReads searches a clonal sequencer fasta data files for sequences containing user defined short sequence.
    • Gene genotyper will screen a clonal sequencing fasta data file against a list of know SNPs and output their genotypes.
    • IlluminaQC reads all the *qseq.txt files in a folder and finds the average PHRED score for each position in the sequence read
  • MethyViewer is an updated version of CpGViewer and is able to screen other methylation sites such as GpC, CpNpG or any user defined site.
  • QSVanalyser calculates the relative ratio of two highly homologous DNA sequences that differ at a few positions.


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