Table 1. Summary of the number of reads generated by 454 pyrosequencing before and after processing and assembling.

Sample	Raw reads	Reads after removal of: exact duplicates, short-reads, low-complexity, human, and bacterial contamination	Reads after assembly (Newbler)	Viral reads tBASTX (unassembled) E value <10−3, cut-off 0.8	Viral reads tBASTX (assembled) E value <10−3, cut-off 0.8	Viral reads MetaVir (unassembled) E value <10−3	Viral reads MetaVir (assembled) E value <10−3
C1	3,196	901	605	272	129	195	98
C2	53,420	40,387	3,088	3,606	480	2,641	374
C3	43,543	33,153	2,060	3,459	111	3,411	78
C4	67,822	50,393	2,758	4,392	454	4,087	355
C5	52,747	44,501	3,241	5,746	316	6,444	277
C6	54,838	49,263	1,813	5,198	147	2,769	101
C7	39,990	23,228	890	3,343	111	1,717	55
C8	62,063	53,874	2,467	6,214	323	6,896	286
C9	26,145	23,325	870	1,576	113	1,899	116
C10	29,035	19,414	1,540	2,173	96	1,266	46
IC1	12,820	10,170	715	1,129	31	1,143	25
V1	12,480	10,875	2,759	3,555	666	3,518	555
V2	28,292	13,435	1,801	4,360	533	4,048	426
V3	16,877	14,478	2,138	3,092	603	3,372	518
V4	32,269	30,928	2,200	797	153	1,311	164
V5	18,556	17,619	1,400	1,136	63	1,402	67
V6	18,620	14,179	6,474	2,225	995	2,066	722
V7	12,707	11,693	1,199	4,146	193	4,315	157
V8	16,595	15,278	2,332	850	270	773	230
Total	602,015	477,094	40,350	57,269	5,787	53,224	4,648

The number of reads with homology to viral hits is compared between our tBLASTX approach and MetaVir, using unassembled and assembled reads.

C1–C10, CD fecal samples; IC1, CD intestinal sample; V1–V8, control samples.