Table 1.

Test Datasets and Sequencing Statistics

	E. coli	B. pseudomallei	S. cerevisiae	D. melanogaster
Size (Mbp)	4.6	7	12.1	22.4
Chromosomes	1	2	16	1
Reads (length, insert size, coverage)	80 bp, 300±30 bp 40×	100 bp (454 reads) 20×	80 bp, 300±30 bp 40×	80 bp, 300 ± 30 bp 40×
Paired-reads (length, insert size, coverage)	50 bp, 10±1 Kbp 2×	20 bp, 10±1.5 Kbp 2.8×	50 bp, 10±1 Kbp 2×	50 bp, 10 ± 1 Kbp 2×

Note that, for a library where insert size is μ ± σ, τ was set to μ + 6σ and in all cases l_min was set to 500 bp. For the synthetic datasets, 10% of the large-insert library reads were made chimeric by exchanging read-ends at random.