Step 21: Conclusions
Summary of SNP/INDEL search and oligo design:
Our "Python DIS Pipeline" works fine to detect SNP/INDEL candidates and possible
paralogs in a given CAP3 EST assembly represented by two or more genotypes.
Chromatograms and Phred quality scores are not required to process data
using our approach.
In general, it is possible to use this pipeline for assembly other than CAP3
if the corresponding input files for Python_CAP3_contig_poly_DIS_Feb_27_2004.py
script are available.
Pipeline does not provide full information about all polymorphic sites
in a given assembly, however, search for SNP/INDEL candidates is reliable.
Visualization by Py_ContigViewer helps a lot to validate "DIS" candidates.
Pipeline is extended to semiautomatic oligo design by Primer3 program.
It has been successfully tested in several labs with different datasets.
Probably, pipeline is not perfect yet. However, source code is freely available
and can be modified to improve functionality.