In the MultiMite test, 9 target X sample combinations were flagged as hitting a repeat and further assembly was stopped at iteration 2. In actuality this occurred because a small number of reads were recruited on the first iteration followed by a large number on the second. In 8 of 9 cases a reduced number of contigs was produced on iteration 2 compared to 1, and in the 9th case the number was equal.
Based on these results:
Set up a new criteria for repeat detection which includes num contigs. For example:
if NumReads > lastNumReads * multiplier AND NumContigs > lastNumContigs:
isRepeat = True
This should guard against most cases of false repeat detection.
In the MultiMite test, 9 target X sample combinations were flagged as hitting a repeat and further assembly was stopped at iteration 2. In actuality this occurred because a small number of reads were recruited on the first iteration followed by a large number on the second. In 8 of 9 cases a reduced number of contigs was produced on iteration 2 compared to 1, and in the 9th case the number was equal.
Based on these results: Set up a new criteria for repeat detection which includes num contigs. For example:
if NumReads > lastNumReads * multiplier AND NumContigs > lastNumContigs: isRepeat = True
This should guard against most cases of false repeat detection.