And we observed astonishing number of repeats in results. Repeats are common in nature and the improved ability to resolve repeats is one of the strengths of long-read sequencing. But the repeats we found didn't look convincing and likely underlined other issues.

Accurate reconstruction of genomic variation is essential to associate within-population structural differences to ecological or evolutionary phenotypes. But we observed serious haplotyping errors, where assemblers created chimeric constructs or did things biologists wouldn't expect.

We observed cases of premature circularization. VERY OFTEN. Catching premature circularization can be easy in some cases, but very difficult in others.

We observed chimeric contigs where the assembly software reported a single contig that brought together sequences from two distinct taxa, sometimes three or more, and even sequences that belonged to distinct domains of life.

But then we learned that Jill Banfield's group was dealing with similar issues in soil samples. At that point we decided to take a deeper look at our long-read assemblers, and used the datasets they used, and added some novel ones into the mix to re-evaluate them.