SAUTE: sequence assembly using target enrichment

BMC Bioinformatics

Table 2 Number of benchmark proteins in orthologous pairs recovered perfectly or as essentially complete by coding regions assembled by different methods

Read	Target	Ortho pairs		Perfect					Essentially complete
set	species	Count	Median	rnaSP	Trinity	SPAln	Clust	SP10	rnaSP	Trinity	SPAln	Clust	SP10
Corn	Z. marina	2710	57.78	537	539	213	312	548	1434	1450	1037	916	1344
	A. tauschii	2888	77.94	550	555	410	510	664	1491	1514	1360	1395	1552
	S. bicolor	2871	92.60	549	554	463	572	666	1488	1507	1399	1464	1549
Thale	P. axillaris	2287	61.56	1616	0	598	1216	1598	1902	0	1364	1503	1933
cress	B. rapa	2312	85.18	1636	0	1255	1405	1870	1924	0	1879	1697	2107
	A. thaliana	2317	100.00	1640	0	1689	1375	1951	1928	0	1991	1668	2122
Worm	T. spiralis	2194	40.92	1588	0	156	646	1046	1940	0	638	867	1269
	C. briggsae	3112	86.46	2230	0	1216	2016	2436	2707	0	2336	2486	2731
	C. elegans	3130	100.00	2244	0	2276	2176	2640	2724	0	2720	2624	2851
Mouse	P. cinereus	9005	77.04	2824	2880	1954	2185	3308	3790	3743	3393	3202	4274
	H. sapiens	9109	86.73	2831	2889	2212	2568	3469	3803	3753	3537	3640	4356
	M. musculus	9177	100.00	2858	2914	2862	3001	3686	3832	3781	3850	3982	4460
Human	P. cinereus	8984	78.80	2796	3107	2144	2206	3340	4383	4645	3995	3551	4792
	M. Musculus	9109	86.73	2824	3134	2372	2401	3496	4425	4684	4168	3784	4875
	H. sapiens	9157	100.00	2839	3152	2994	2601	3760	4448	4708	4630	4032	5013

SAUTE_PROT low (SP10) with maximum of 10 variants reported per graph, SPAligner (SPAln), and CLUSTER (Clust) used proteins from the target species for assembling the read set. rnaSPAdes (rnaSP) and Trinity are de-novo assemblers. The median percent identity between orthologous protein pairs varies from 40.92 to 100%. In each row, count for the method that finds the largest number of proteins as perfect or as essentially complete are in bold

ISSN: 1471-2105