Table 1.

Contig sets

Contig Organism	# Contigs	Total Length	N50 Contig Size
C. aurimucosum ATCC 700975	108	2 716 204 bp	96 704 bp
C. kroppenstedtii DSM 44385	9	2 434 935 bp	546 376 bp
C. urealyticum DSM 7109	69	2 294 755 bp	86 391 bp

The three contig sets that were used to evaluate our algorithm. All corresponding genomes have already been finished. The N50 contig size gives the size of the largest contig such that at least half of the total size is covered by contigs larger than that contig. This measure is more robust than the mean or median if many small contigs exist.