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Quality control, detagging and reformatting of clonal sequencing data

AgileQualityFilter performs a number of pre-alignment tasks on sequence data from an Illumina GA-II clonal sequencer. The primary function of AgileQualityFilter is to remove low quality sequence data before alignment to a reference sequence. It can also performs the secondary roles of formatting the data from *.qseq.txt, *.fasta or *.fastq files to either the *.fasta or *.fastq file formats. If the reads are tagged with 5′ index tags (“barcodes”), the program can export the detagged data to a specific file.

AgileQualityFilter reads the PHRED quality string for each sequence and identifies the position of bases where the quality falls below a user-defined cut-off value. These positions then become uncalled positions and are subsequently exported as 'N's. It is possible to limit the number of uncalled positions in a read, with the sequence truncated if it exceeds the user-defined value. It is also possible to identify reads whose median quality score falls below a user-defined value; these reads can be either rejected or truncated so that the median quality score of the remaining sequence is no longer below the cut-off value.


The AgileQualityFilter user guide can be found here.


The AgileQualityFilter program can be downloaded from my departments web site here.

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