Workshop on Genomics 2016 Assembly Lab report

	A	B	C	D	E	F	G	H	I	J	K	L
1		assembler used	Dataset (500k or full? pacbio?)	Value(s) of k, if applicable	number of scaffolds/contigs (larger than 0 bp)	total size of assembly (Kbp) ("Kbp" means: times 1000 base pairs)	scaffold NG50 (Kbp)	scaffold NGA50 (Kbp) (if you have not computed this metric you are not eligible for the contest!)	contig N50 (Kbp)	(optional) number of proteins predicted by Prokka	comments / extra parameters used

2	Maggie Sefton	SPAdes	Full+Pacbio	5,7,11,15,21,25,33,55,69,77				running	running		--careful, 2 pacbios [ k values of 5, 7 and 11 are probably not going to be informative, but i'm holding my breath to see those results -- Rayan]
3	Wenche Eikrem	GATB-Pipeline	500k	default		4020			3352		[I don't believe this contig N50! --rayan]
4	Best Guy	Spades							1337		;-)
5	Rayan	Spades	full+pacbio	default	28	4067	974	973	974		Additional scaffolding with SSPACE-Longread
6	Abby Schiff	SPAdes	full + pacbio	default	53	4063	806	806	950		--careful
7	Mario Vicente	spades	full + pacbio	default	53	4063	806	806	950		--careful
8	Peter Christ	SPAdes	full+pac	default	53	4059	806	806	950		company secret
9	Sergio	SPAdes	full + pacbio	multi-k	35	4059	806	806	950	3579
10	Jeremias Brand	Spades	full + pacbio	default	53	4063		806	950		-really_careful
11	Catarina Silva	SPAdes	full + pacbio	default	36	4054			940
12	Gema Alama	Spades	Full+Pacbio	21,33,55	36	4054	806	806	939		careful
13	Rosario Castañeda	SPAdes	full + pacbio	multi-k	54	4058	806	806	939	3572	--careful
14	Jen Maier	SPAdes	full + pacbio1	default	36	4054			939		--careful
15	Tim Nice	SPAdes	full + pacbio	27,39,51,63,75	44	4060	810	747	810		--careful
16	Reinder Radersma	SPAdes	Full+Pacbio	21,33,55,75	45	4065	810	746	810		--careful
17	Tim Nice	SPAdes	full + pacbio	21,33,55,77	46	4060	807	747	807		--careful
18	Krystyna Cwiklinski	SPAdes	Full +pacbio	21,31,33,55,77	50	4060	806	746	806		full + 2 PacBio files
19	Stefan Ciaghi	SPAdes	full + pacbio1	21,33,55,77,127	62	4049	638	638	638		--careful
20	Tomas Panek	SPAdes	full + pacbio 1	default	80	4048	638	345	638		--careful
21	Greg McCracken	SPAdes	full+pacbio			4053		638	638		--careful, illumina+pacbio data, custom k values
22	Hugo, Aurelie, Andrea	SPAdes	full + pacbio	27,31,37	55	4042	637	637	637		pacbio
23	Emelie Nilsson	SPAdes	full + pacbio 1		79	4048	637	345	637		--careful
24	Rosario Castañeda	SPAdes	full + pacbio	multi-k	80	4055	637	345	637	3580	--careful
25		SPAdes	Full + pacbio	default	80	4055	637	345	637		--careful
26	Patrik Rödin Mörch	Spades	500k + pacbio	Defaul	60	4059	481	369	481	3589	--careful
27	Aapo Kahilainen	SPAdes	500k + pacbio (1 & 2)	default	40	4054	481	358	481		--careful
28	Reinder Radersma	SPAdes	500k + pacbio	default	59	4060	418	370	481
29	Marie Jalovecka	spades	500k + pacbio	default	60	4055			481		illumina + pacbio 2 files
30	Josephine Braun	SPAdes	500k + pacbio	21,31,41,51,61,71	69	4063	478	320	478		--careful; illumina -1 and -2; 2 PacBio files
31	Willian Silva	SPAdes	500k + pacbio	default	48	4045	274	470	470	3542	--careful
32	Beatriz Willink	SPAdes	full+pacbio	25,37,59,81	51	4054	428	428	428		--careful
33	Beatriz Willink	SPAdes	Full + pacbio1	25,37,59,81	64	4047	251	249	428	3570	--careful
34	Barbora Kalousova	SPAdes	500k+pacbio	Default	62	4055	358	358	358	3582
35	Dagmar Cizkova	SPAdes	500k+pacbio	Default	62	4055	358	358	358	3582
36	Sergio	SPAdes	500k + pacBio	multi-k	39	4060	358	358	358		Illumina + PacBio
37	Sergio	Spades	500k and PacBio	Multi-k	39	4060	358	358	358		Illumina + PacBio
38	Catarina Silva	SPAdes	500k + pacbio	default	42	4055			358		Not careful
39	Katerina Svehlova	Spades	500k+pacbio	default	62	4055			358	3582	also 3582 for scaffolds.fasta
40	Lur Epelde	SPAdes	500k +pacbio	Default	41	4060			358
41	Oscar Rollano Penaloza	SPAdes	500K + Pacman		42	4055			358
42	Sara Hardardottir	SPAdes	f	default	83	4045			354
43	Jamie Stevens	SPAdes	500 + pacbio_1		83	4045			345
44	Eryn McFarlane	SPAdes	500K +pacbio	21, 51, 71	71	4061	320		287
45	Aapo Kahilainen	SPAdes	full + pacbio 1 & 2	21,31,41,51,61,71,81,91,95	39	4022	275	240	275		--careful
46	Sandra Lorena Ament	SPAdes	500k + PacBio	21,33,55	79	4051	274	274	274
47	Tim Nice	SPAdes	500k + pacbio	default	80	4051	274	274	274	3570	--careful
48	Tracy Meiring	SPAdes	full+Pacbio	21,37,59	105	4048	274	248	274
49	Miya Qiaowei Pan	SPAdes	500k	default	49	4052	274		274	3541	--careful
50	Jamie	SPAdes	500 + pacbio	31	102	4037			274
51	Jamie Stevens	SPAdes	500k + pacbio_2		102	4038			274
52	Hanna Berggren	SPAdes	full	default	159	4030	235	198	235
53	Jen Maier	SPAdes	full	default	87	4011	235	197	235	3539	--careful
54	Stefan Ciaghi	SPAdes	high cov	21,33,55,77,127	137	4020	198	193	198		--careful
55	Reinder Radersma	SPAdes	500K + pacbio	21,33,55,75	72	4052	192	192	192
56	Aapo Kahilainen	SPAdes	500k + pacbio 1 & 2	21,31,41,51,61,71,81,91,95	52	4024	167	167	167	3552	--careful
57	Abby Schiff	SPAdes	500k	25,53,65,79,91	76	4026	166	141	166		illumina + pacbio (file 1 only)
58	Sergio	SPAdes	500k	18	88	4015	165	155	165		Illumina only
59	Emelie Nilsson	SPAdes	500k	default	172	4014			164	3544
60	Hanna Berggren	SPAdes	500k	default	172	4014			164
61	Marta Vargas	SPAdes	500k		172	4014	98794		163	3531
62	Reinder Radersma	SPAdes	500k	default	172	4014	163	155	163	3544
63	Ana Millanes	SPAdes	500k	default	172/173	4014	163	134	163
64	Jeremias Brand	SPAdes	500k	Default	176	4012		155	163		-careful
65	Anna Nordén	SPAdes	500k	21,33,55,77,127	90	4031			163	3543
66	Reinder Radersma	SPAdes	500k		175	4012			163	3542	--careful
67	q	SPAdes	500k + pacbio	21,33,55,77	85	4046			161		Illumina + PacBio (the one ending on 5, not 6) --carful
68	Maggie Sefton	SPAdes	500k/pacbio	5,15,21,33,55,77	59	4047	156	156	160		--careful, PacBio (1 file)
69	Disa Bäckström	SPAdes	500k+pacbio	default	86	4041			156		--careful
70	Jen Maier	SPAdes	500k	default	92	4011	155	134	155	3541	--careful
71	Oliver Gast	SPAdes	500k	21,33,55	175	4014	155	134	155
72	Tim NIce	SPAdes	500k	default	177	4030	155	134	155	3544	--careful
73	Barbora Kalousova	SPAdes	500k	Default	175	4013	155		155	3543
74	Dagmar Cizkova	SPAdes	500k	Default	175	4013	155		155	3543
75	Gema Alama	Spades	500K	21, 33, 55	92	4011			155		--careful
76	Jamie Stevens	spades	500k		175	4014			155
77	Tomas Panek	SPAdes	500k	default	175	4014			155	3543
78	Willian Silva	SPAdes	500k	21,33,55,77	86	4021	143	134	143		--careful	Who deleted my name? :(
79	Emelie Nilsson	SPAdes	500k	21, 33, 55, 77	137	4021			143	3543	--careful
80	Maggie Sefton	SPAdes	500k	5,15,21,33,55,77	90	4032			135		--careful
81	Abby Schiff	SPAdes	full + pacbio	21,33,45,55,67,77,99	117	4024	134	134	134		Illumina + both PacBio
82	Gema Alama	Spades	Full+Pacbio	21,33,55,77,99,127	103	4019	134	134	134		careful
83	Stefan Ciaghi	SPAdes	500k	21,33,55,77,127	140	4019	134	132	134		--careful
84	Ben Rutter	SPAdes	500k	5,21,33,55,77	89	4019			134
85	Eryn McFarlane	SPAdes	500k	21, 51, 71	157	4033			134
86	Disa Bäckström	GATB-Pipeline	Full	21,31,41,51,61,71,81,91,101	125	4019	130	111	130
87	Disa Bäckström	SPAdes	full + "trusted contigs" ( contigs >50kb from GATB-assembly)	21,33,55,71	412	4049	121	121	126		--trusted-contigs <contigs >50Kb long from GATB assembly> \| Note: Did not help, but probably made SPAdes break the contigs in the same places as GATB did.
88	Zihan Dai	SPAdes	500k	21,55,77	143	4032	125	123	125	3543	--careful
89	Abby Schiff	SPAdes	500k	25,53,79	132	4020	121	121	124	3541	Used --careful
90	Ben Rutter	SPAdes	500k	21,33,55,77,127	95	4017			121
91	Aapo Kahilainen	SPAdes	500k	21, 33, 55, 77, 91	95	4016	110	108	120		--careful; Tried also eralier with a filtered one, but managed to crash the run (because defined too large k-mer size based on the unfiltered file)
92	Amit Roy	SPAdes	500k	21,33,55,77,85,127	103	4012			109		--careful
93	Disa Bäckström	GATB-Pipeline	Full	21,41,61,81,101	147	4014	108	108	108
94	Tomas Panek	gatb	full	default	147	4014	108	108	108
95	Disa Bäckström	GATB-Pipeline	500k	21,31,41,51,61,71,81,91,101	141	4055	108	98	108	3567
96	Lur Epelde	SPAdes	500k	Default	121	4006	108		108	3534
97	Amit Roy	SPAdes	500K	21,33,55,77,87, 127	102	4013			108		-- careful
98	Jeremias Brand	GATB	Full	default	110	4014			108
99		GATB-Pipeline	500k	21,55,77	159	4030	101		103	3539
100	Maria Cortazar	GATB-Pipeline	500k	Default	163	4008	1012(unlikely)		101