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jts / sga

de novo sequence assembler using string graphs
http://genome.cshlp.org/content/22/3/549
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ASQG Format clarification #90

Closed mariokostelac closed 9 years ago

mariokostelac commented 9 years ago

I am working on ASQG to AFG file converter and it's not very clear what means when I have an overlap that looks like:

0 30 100 (start1, end1, len1)
0 20 200 (start2, end2, len2)

and second overlap is reversed.

Does it mean that overlap looks like

    ----->   (A)
<..... (*B)

where *B is actually a reversed complement of some read B from input set?

jts commented 9 years ago

Yes, your picture is correct.

To put it in string comparison terms, the coordinates indicate A[start1:end1] == rc(B[start2:end2]) with inclusive end coordinates.

mariokostelac commented 9 years ago

Thank you @jts.