AgileSMPoint
Identification of somatic sequence variants at predetermined positions using unaligned sequence data.
AgileSMPoint identifies somatic sequence variants occuring at specific positions in unaligned next generation sequence data.
Somatic mutations at specific nucleotide positions have been found to lead to or play a role in the progression of many diseases most notably in cancers. For instance mutations at codons 12 and 13 in KRAS are often associated with the development of many types of cancer. The detection of somatic mutations is hindered by the presence of varying amounts of normal tissue in the DNA sample. Consequently, important somatic mutations may occur at levels of only 1 or 2% in the analysed DNA sample. To aid the detection of somatic mutation we have developed the program AgileSMPoint which screens next generation sequence data derived from PCR amplicons that contain the mutation hotspots of interest. AgileSMPoint does not require the data to be prealigned and is able to import sequence data from either *.fasta or *.fastq files. The sequence data may contain reads from a large number of different amplicons each containing a number of different hotspots.
If the PCR products are longer than a typical read length it is possible to sequence them using paired ends and then combine the read data in a single full length read using AgilePairedEndReadsCombiner.
Guide to use of AgileSMPoint:
The AgileSMPoint user guide can be found here.
Download
The AgileSMPoint program can be downloaded here.