AgileSMAll

Identification of somatic sequence variants in unaligned sequence data.

AgileSMAll identifies rare somatic variants in a heterogenious sample. The regions of interest must first be amplified by PCR and then clonally sequenced across the positions of interest. Unlike AgileFastaVariantFinder, this program does not look at specific positions but instead looks at all positions present in the sequence data. Since the sequence data, even when using multiplexed PCR products is derived from a relatively small population of read types, AgileSMAll is able to identify the origin of each read. Consequently the sequence data is not aligned to a genome before analysis. 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 AgileSMAll:

The AgileSMAll user guide can be found here.

Download

The AgileSMAll program can be downloaded here.