Table 1. Comparison of Oxytricha macronuclear genome assemblies.

Assembler	PE-Asm/SSAKE	IDBA	ABySS	Final Assembly
Assembly size (bp)	47,753,834	57,684,531	78,039,140	67,172,481
Number of contigs	22,840	47,882	34,330	22,450
Number of telomeres	4,883	3,929	30,071	38,724
N50 (bp)	2,579	1,938	3,473	3,736
Mean contig length (bp)	2,090	1,204	2,273	2,982
2-telomere contigs	683	262	6,421	15,993
Mean 2-telomere contig length (bp)	3,070	3,148	3,243	3,187
Number of 1-telomere contigs	3,497	3,376	16,399	5,303
Mean 1-telomere contig length (bp)	2,773	2,260	2,182	2,694
Number of 0-telomere contigs	18,660	44,244	11,510	1,154
Mean 0-telomere contig length (bp)	1,927	1,112	1,861	1,655
Number of multitelomere contigs	20	28	776	1,279
Mean multitelomere contig length (bp)	3,438	3,436	5,049	4,208
Raw PE read coverage	78.7%	87.2%	98.0%	98.0%
PE telomeric read coverage	45.4%	42.4%	91.8%	91.0%
Raw SE read coverage	72.5%	80.5%	88.2%	88.5%
SE telomeric read coverage	29.0%	27.5%	64.4%	69.6%

The 2-telomere contigs have both 5′ (CCCCAAAACCCC; with degenerate bases—see Materials and Methods) and 3′ (GGGGTTTTGGGG; with degenerate bases) telomeric repeats. Note that 2-telomere contigs are mostly complete nanochromosomes but may also be alternatively fragmented nanochromosomes with one or more additional missing ends and that multitelomere contigs may be either alternatively fragmented nanochromosomes or nanochromosomes with internal telomere-like repeats. Raw read coverage is calculated from LAST (default parameters; version 159; contig telomeres were masked) matches (≥70 bp long and ≥90% identical) to the assemblies. Read coverage was calculated for the total high quality PE sequence data set and one of the three lanes of SE sequence data. Of the PE reads 13% were telomere bearing, as opposed to 4.7% of the SE reads.