I am trying to learn how to perform virtual DNA sequencing procedure that includes base calling, sequence assembly, mapping assembly, and contig mapping. Please suggest a simple way of performing this procedure.
Alain Coletta
Do you mean like this? http://hshgp.genome.washington.edu/student_activities/virtseq1.htm
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Matej Lexa
You can use ART or GRINDER to simulate sequencing reads from a specific machine:
http://www.ncbi.nlm.nih.gov/pubmed/22199392
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384353/
Then you can apply the common processing steps all the way to mapping, assembly or variant calling that are amply described elsewhere. One of several possible workflows is given on Bioconductor webpages: http://www.bioconductor.org/help/workflows/high-throughput-sequencing/
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