We recently finished an assembly of Guignardia bidwellii paired end DNA reads using Abyss and refined the results with SSpace. However, we were not quite satisified with the results (still to many contigs).
We are now considering generating new libraries with larger insert sizes between paired ends to resolve repeats. Is there a genereal guideline for choosing those insert sizes? From what I understood so far, an optimal insert size would be larger than the length of the largest repeat appearing in the genome (is this correct?).
Sadly, we do not have too much information about the genome for estimating the size of repeats in the genome. Is there some way to make an eductaed guess based on the Abyss-output files (like the contig linkage graph) of our last assembly? Or should we simply go for the largest insert size possible?
Thank your for answers
Martin
We are now considering generating new libraries with larger insert sizes between paired ends to resolve repeats. Is there a genereal guideline for choosing those insert sizes? From what I understood so far, an optimal insert size would be larger than the length of the largest repeat appearing in the genome (is this correct?).
Sadly, we do not have too much information about the genome for estimating the size of repeats in the genome. Is there some way to make an eductaed guess based on the Abyss-output files (like the contig linkage graph) of our last assembly? Or should we simply go for the largest insert size possible?
Thank your for answers
Martin
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