One DNA strand
gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac ggaaccattg ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca gtagtcagct

DNA reads
gatcctccat ata
ggt atctccacct
atacaacggt atc
cct caggtttaga
atctccacct cag
aga tctcaacaac
caggtttaga tct
aac ggaaccattg
tctcaacaac gga
aac ggaaccattg
ggaaccattg ccg
gag acagttaggt
ccgacatgag aca
ggt atcgtcgaga
acagttaggt atc
aga gttacaagct
atcgtcgaga gtt
gct aaaacgagca
gttacaagct aaa
gca gtagtcagct
aaaacgagca gta

example of OUTPUT:
gatcctccat atacaacggt atctccacct cag

gatactgcat atactactgt atc......

diferrence in location: 3,6,14,17

The reads can be align using 3-mer/ 3 character at the front and end of each reads string.
1. Align the reads above into a single DNA strand.
2. Find the location of difference in the two strand.

Does anyone actually know what the question is? Does the OP?

Probably not, considering the non-existent quality of the "spec". As someone once said "If it was easy, anyone could do it."...

This article has been dead for over six months. Start a new discussion instead.