Table 2.

Performance evaluation of AlignGraph

Upstream assembler	Contig set	N Contigs4	N505	N covered bases6	Average length7	Maximum length8	MPMB9	Average identity10 (%)
(a) Contigs of A.thaliana genome
Velvet	All1	30 037	3515	82 844 417	2668	27 792	22.2	95.2
	Extendable2	8615	4148	28 007 451	3262	27 398	0.3	97.6
	Extendable + AlignGraph3	5751	7876	32 467 110	5521	49 768	1.6	94.8
ABySS	All	30 972	2559	69 432 667	2206	29 760	13.4	97.2
	Extendable	11 693	2820	28 885 212	2454	16 343	0.5	98.7
	Extendable + AlignGraph	8427	5484	35 859 786	4151	25 321	1.1	95.8
(b) Contigs of human chromosome 14
ALLPATHS-LG	All	4383	38 590	83 849 397	19 201	240 764	0.3	98.9
	Extendable	1674	39 851	35 746 095	20 806	200 495	0.1	98.9
	Extendable + AlignGraph	785	71 847	36 441 001	45 358	305 880	0.0	97.5
ALLPATHS-LGc	All	3856	43 856	83 860 939	21 818	275 446	0.2	99.3
	Extendable	1296	45 719	31 457 201	24 346	275 446	0.1	99.5
	Extendable + AlignGraph	608	86 613	34 614 465	54 406	294 615	0.0	96.9
SOAPdenovo	All	10 865	16 855	80 135 941	7623	147 494	5.9	94.9
	Extendable	5613	17 412	45 246 077	8223	141 981	0.9	96.4
	Extendable + AlignGraph	3469	32 881	52 861 640	15 271	219 841	0.5	95.0
MaSuRCA	All	19 034	5767	75 497 302	3802	53 837	13.9	98.9
	Extendable	9241	6047	38 842 517	4199	51 249	0.2	99.2
	Extendable + AlignGraph	5665	11 590	43 930 184	7666	66 758	0.4	98.1
CABOG	All	3118	46 523	84 989 190	27 401	296 888	0.3	97.3
	Extendable	1692	45 669	46 499 763	27 089	296 888	0.0	98.7
	Extendable + AlignGraph	701	101 907	50 527 605	70 362	443 952	0.1	97.6
Bambus2	All	11 219	8378	64 011 072	5764	449 449	3.1	89.9
	Extendable	6995	7521	37 857 989	5439	62 798	0.3	97.6
	Extendable + AlignGraph	2722	19 989	39 147 357	14 176	86 154	0.5	96.5
(c) Scaffolds of human chromosome 14
SOAPdenovo	All	3902	391 693	85 417 248	24 397	1 852 152	1.0	82.9
	Extendable	901	387 309	40 296 035	47 526	1 019 659	0.1	84.5
	Extendable + AlignGraph	767	544 209	47 823 279	63 525	2 246 638	0.1	81.0
MaSuRCA	All	721	580 822	65 433 305	63 876	2 943 966	1.3	57.2
	Extendable	101	289 703	5 554 781	52 820	1 516 804	0.0	81.9
	Extendable + AlignGraph	78	316 946	6 986 224	86 552	1 573 741	0.0	83.4
CABOG	All	471	387 876	81 163 688	176 590	1 944 475	0.1	91.9
	Extendable	146	358 688	29 372 033	200 539	1 905 529	0.0	98.2
	Extendable + AlignGraph	67	906 407	33 708 925	481 712	2 051 503	0.0	94.1
Bambus2	All	569	319 334	64 378 693	116 582	1 477 847	0.1	77.4
	Extendable	66	272 436	6 949 338	119 858	641 463	0.0	92.0
	Extendable + AlignGraph	80	377 905	8 963 132	114 852	812 353	0.1	85.4

(a) Genomic PE reads from A.thaliana were assembled with Velvet and ABySS. The resulting contigs were extended with AlignGraph using as reference the genome sequence from A.lyrata. (b–c) The subsequent panels contain assembly results for the human chromosome 14 sample from the GAGE project where the chimpanzee genome served as reference. (b) Contig assembly results are given for the de novo assemblers ALLPATHS-LG, ALLPATHS-LGc (in cheat mode), SOAPdenovo, MaSuRCA, CABOG and Bambus2. (c) Scaffolded assembly results are given for SOAPdenovo, MaSuRCA, CABOG and Bambus2. The results are organized row-wise as follows: the number of initial contigs obtained by each de novo assembler¹, the ‘extendable' subset of the initial contigs that AlignGraph was able to improve², and the extension results obtained with AlignGraph³. The additional columns give the number of contigs⁴, N50 values⁵, the number of covered bases⁶, the average⁷, and maximum⁸ length of the contigs, the number of misassemblies per million base pairs (MPMB)⁹, and the average identity among the true contigs and the target genome¹⁰. More details on these performance criteria are provided in Section 3.1.5.