As I understand, prior to scaffolding using long mate-pair reads, runs of N's or A/G/C/T's cannot exceed the length of the reads used for assembly (in this case 101bp). After scaffolding there are long series of N's as a result of contigs being joined together.
Can there also be long runs of A/G/C/T's after scaffolding? This is what I am seeing. I thought perhaps that joining contigs together ending in homopolymer repeats might, instead of an N, result in an A being used for example if those two contigs ended with long runs of A.
ABySS-1.3.4 was used for assembly and SOAPdenovo2 was used for scaffolding.