Workshop on Genomics 2014 Assembly Lab report

	A	B	C	D	E	F	G	H	I	J	K
1	Your name	assembler used	Dataset used (subsampled or full?)	value of k	number of scaffolds/contigs (larger than 0 bp)	total size of assembly (Kbp)	scaffold N50 (Kbp)	contig N50 (Kbp)	(optional) number of proteins predicted by Prokka	comments / extra parameters used

2	Agata	Minia	sub	31	1086	3679956		5.639	3211
3	Anders	Minia		20	3882	3874536	-	2.395		testing testing
4	Angela	Minia	sub	31	1086	3679956		5.639	3211	min_abundance 5
5	Angela_second run	Minia	full	29(from Kmergenie)	340	3369570		27.332	3409	playing with k had much less effect than using full vs. sub-sampled dataset
6	Anja	SPAdes	subsampled	default	296 scaffolds / 297 contigs	3966148	64334	64.334	3445	--careful option
7	Anke	Minia	subsampled	31	1086	3679956		5.639	3211
8	Anna	Velvet	subsample	21	2751	3002		1.206
9	Anna2	Velvet	full	21	30622	1228		0.695
10	Antje	Minia	subsampled	31	1086	3679		5.639	3211
11	Bartek	minia	subsampled	25		4280,3		4,18
12	Berrit	Minia	subsampled	27	1174	3656	---	4.884		min abundance 3
13	Berrit4	Minia	sub	97	610	3.969	---	0.621	1627	min abund is 5 (Berrit)
14	Britta	Minia	subsampled	31	1086	3679956		5639
15	Catherine	Velvet	subsampled	31	794	3742		18.8	3303	-exp_cov auto
16	Catherine 2	Velvet	full	31	598	4101		24.4		-exp_cov auto
17	Cris	Minia		31	1086	3679956		5639	3234
18	Dag									just testing
19	dan	Minia	subsampled	31	1086	3679956		5639
20	dan	velvet	subsampled	77	589	3822697
21	dan	spades	subsampled	21,33,65	476	3920330	58.67	58.67	3472
22	Debbie	velvet	subsampled	33	410	3811.518	19.438
23	Debbie	SPAdes	subsampled	21, 33, 55	488	4009.292	57.886		3472	careful option
24	Debbie	SPAdes	full	31, 59	763	4189.293		204.282		careful
25	Dick	Minia	subsampled	31	1086	3679956		5639
26	Doug	Velvet	subsampled	31	1271			1.023
27	Elin Videvall	Velvet	subsample	21	2758	3005	1.2
28	Elin Videvall	Velvet	full	61	2096	3614		2.2	3459
29	Elin Videvall	SPAdes	full	61	140	3952	195.237			SNYGGT!
30	Elin Videvall	SPAdes	full	101	129	3954	106.526
31	Elin Videvall	SPAdes	full	85	124	3954	113.887
32	Ellie Bors	Minia	subsampled	27	1174	3656711		4.884	3204
33	Ellie Bors	SPAdes	subsampled	31	289	3898818	43.16		3459
34	Emilia	Minia	subsampled	31	2074	3679956
35	Emilie_Audrey	velvet	sub	51	1100	3990955		12.69
36	Emily	Minia		31	1086	3679956	5.639		3211
37	Eva	minia	subsampled	31	2074	3864		5639	3211
38	Fernando	SPAdes	subsample	61	228	3919866	50924	64.334	1126
39	Georg	Minia	subsample	29	1059	3687615		5.761	3221	test
40	Gerard1	Minia	subsampled	21	1691	3844659		8256		min abundance 3
41	Gerard2	Minia	subsampled	31	1007	3870341		16286		min abundance 3
42	Gerard3	Minia	subsampled	31	683	3920079		13.092	3430	min abundace 5
43	Guy Leonard	Ray	full	101
44	Hannu	Minia		27	1344	3905		11.2
45	Hermes	Spades	full	n/a	222	4080001	88651	61384
46	Ida	Velvet	subsampled	43	4930	3721		3.8
47	Igor	Velvet	subsampled	31	596	3805.55		23.65	3311	91.13% coverage
48	Igor 2nd try	Velvet	full	31	564	3813.69		23.65	3316	93.22% coverage
49	Igor 3rd try	Velvet	full	kmer genie
50	Ina	Minia	250k	31	1086	3679956		5.639
51	Ina	minia	full	31		3864		29.376
52	Ingrid	Minia	subsampled	32	824	3759211		8463	3294
53	Isotta D'Arrigo	Minia	250K	31	2074	3864482		5639	3211
54	Isotta D'Arrigo	SPAdes	250K	31,55,61,77,99,127	296/297	3968077		64334
55	Iwona	Minia	sub	31	657	3795		11.267	3333	min_abundance 3
56	Jason	Minia	subsampled	31	1086	3679956		5.639
57	Jason	Minia	subsample	25	1002	3690656		6.095
58	Jason	SPAdes	subsampled	31,55,61,77,99,127	213/212	3918.702	50.93	50.93		--careful mode, corrected
59	Jason	SPAdes	full	65	609	4120.69		166.801		--careful mode, corrected
60	Jon Corell	Minia	subsampled	31	5441	2966		1593	2805
61	Jon Corell 2	minia	subsampled	31	6552	2698		1250	2685
62	Jon Tinnert	Velvet	subsampled	31	9451	3266.772		1.381	3213
63	Jon Tinnert 2	Minia	subsample	31	5441	2966.225		1.563	2805
64	Josefine Larsson	Velvet	subsample	41	1513	3710		3.5
65	Josefine Larsson2	Velvet	full	41	2556	3380		16	3429
66	Josie Paris	Minia	full	31	1380	3814.973		16.286		testing
67	Josie paris	ABySS	full	31	1290	3893.423	34.002	34.002	3448	careful parameter and error corrected
68	Josie Paris	spades	full	65	430	4126.502		356.09		Rayan's note: impressive assembly! did you evaluate the # of misassemblies?
69	Jothi Kumar Yuvaraj	Velvet	subsampled	31	9451	3266.772		1.381	3213
70	Jothi Kumar Yuvaraj	Minia	subsampled	31	5441	2966.225		1.563	2805
71	Klara Bojanovic1	Minia	subsampled	31	2074	3864482		5639	3211
72	Klara Bojanovic2	spades	subsampled		297/296	3968077	64.334	64.334
73	Lisa Cohen	Velvet	subsampled	43	1425	3722836		3768	3342	no scaffold file from Velvet (Rayan's note: contigs.fa is actually the scaffolds file, I know, Velvet can be confusing)	Reference comparison: How many large / small misassemblies were made by the assembler? 2 What is the actual genome coverage? 91.579%
74	Lisa Cohen - 2	Velvet	subsampled	29	2704	3195658		1344		no scaffold file from Velvet
75	Lisa Pokorny	minia	full	31	2074	3679.956		5639	3211
76	lu	minia		31	2074	3864	na	5.6		K20 was used, resulted in N50=5639 number of contig 2074
77	Ludovic	spades	250K	It(up to 127)	188	3923	64			Good!
78	Marie	Minia	250K	31	1086	3679956		5.639	3211
79	Marie Krausova	minia	full	31		3949		16	3437
80	Marie Krausova	abyss	full	64	554	3905		59
81	Marie Krausova	velvet	subsampled	31	374	4074		3295
82	Martin	Minia		31	2074	3846682		5639
83	Mats	Minia	subsampled	29	1316	3793		11.1
84	Mats	Minia	full	29	1073	3874		15.7
85	Mats	ABySS	subsampled	40	1325	3826	16.8
86	Mats	ABySS	full	40	1015	3878	43.8		3438
87	Mats	ABySS	full	50	724	3892	52		3440
88	Mats	ABySS	full	64	550	3906	60		3445
89	Max	Minia		31		3679956	5.639	0.188
90	MD	Velveth	full	99	199	3943797	NA	93027		kmer size based on an optimum value between 20 to max -10
91	MD	Minia	subsampled	31	1086	3679	NA	5.639
92	Megan	Velvet	full	31	2182	1659.944		0.749	2985	exp_cov 0 cov_cutoff 0
93	Megan2	Velvet	full	101(from Kmergenie)	2881	2892.638		1.075	3626	Kmergenie run on full dataset, exp_cov 0, cov_cutoff 0
94	Megan3	Velvet	full	61(alternate Kmergenie)	2096	3614.525		2.246		another peak from Kmergenie at 61, exp_cov 0, cov_cutoff 0
95	Megan4	SPAdes	full	101(from Kmergenie)	152	3958.72		105.181	3485	--careful --only-assembler
96	Megan5	SPAdes	full	55,61,65,71,77,99,105	115	3975.22		207.834		running for a thousand years
97	Melis	Velvet	full	31	2182	1659		0.749	2985	After quast with V.cholera genome, 40% genome coverage, 3.9 mismatches per 100kbp
98	Melis 3	Velvet	full	65	168	3850		56		(+ -cov_cutoff auto -exp_cov auto) NG50 is 56 KBp
99	Melis2	Velvet	full	65 (from VelvetOptim on 250K from 20-120 search space)	1961	3674		2.5		After quast with V.cholera genome, 90% genome coverage, 3.2 mismatches per 100kbp
100	Mi	Minia	250K	31	1086	3679956		5.639	3234