OFN_Genomics_Workshop_2016

☰

• Report summary
• Sequence data
• Species identification
• MLST
• Serotyping
• Resistome
• Assembly and annotation
• Reference genome
• Core genome
• Core SNP phylogeny
• Pairwise core SNP distances
• Core SNP density
• Pan genome
• Software versions
• About

Report summary ▲

Download: ⬇jobinfo.csv

Isolates	Author	Date	Host	Folder
18	tseemann	Tue Jun 14 23:04:34 2016	526080-s598782	/mnt/seq/JOBS/BESPOKE/ASM-NGS-Conf-2015/nullarbor

☰

• Report summary
• Sequence data
• Species identification
• MLST
• Serotyping
• Resistome
• Assembly and annotation
• Reference genome
• Core genome
• Core SNP phylogeny
• Pairwise core SNP distances
• Core SNP density
• Pan genome
• Software versions
• About

Sequence data ▲

Download: ⬇seqdata.csv

Isolate	Reads	Yield	GeeCee	MinLen	AvgLen	MaxLen	ModeLen	Phred	AvgQual	Depth	Quality
OFN-57	1790450	424217861	38.5	31	236	251	251	33	34.2	134	✔
OFN-61	1753462	414723445	38.6	35	236	251	251	33	35.1	131	✔
OFN-55	1701422	405832153	38.4	30	238	251	251	33	34.4	128	✔
OFN-62	815450	189091835	38.6	32	231	251	251	33	34.3	59	✔
OFN-60	2073586	481662442	38.5	30	232	251	251	33	35.0	152	✔
OFN-58	274166	65921121	38.1	35	240	251	251	33	30.1	20	✘
OFN-01	1121022	267250486	38.6	31	238	251	251	33	36.3	84	✔
OFN-04	5194186	1180263352	38.6	34	227	251	251	33	35.7	373	✔
OFN-59	1637386	385399586	38.5	34	235	251	251	33	34.5	121	✔
OFN-64	1306728	310863899	38.7	35	237	251	251	33	36.3	98	✔
OFN-65	627360	148114369	38.0	30	236	251	251	33	36.4	46	?
OFN-56	2187320	513849449	38.6	32	234	251	251	33	34.6	162	✔
OFN-68	1000614	236891936	38.1	33	236	251	251	33	36.4	74	✔
OFN-67	727196	172176858	38.3	35	236	251	251	33	36.0	54	✔
OFN-66	1389632	329890768	38.3	32	237	251	251	33	36.4	104	✔
OFN-03	6717352	1513486321	38.6	30	225	251	251	33	35.8	478	✔
OFN-63	1003866	241303994	38.5	34	240	251	251	33	36.2	76	✔
OFN-02	1108224	264208400	38.6	34	238	251	251	33	35.9	83	✔

☰

• Report summary
• Sequence data
• Species identification
• MLST
• Serotyping
• Resistome
• Assembly and annotation
• Reference genome
• Core genome
• Core SNP phylogeny
• Pairwise core SNP distances
• Core SNP density
• Pan genome
• Software versions
• About

Species identification ▲

Download: ⬇identification.csv

Isolate	#1 Match	%	#2 Match	%	#3 Match	%	#4 Match	%	Quality
OFN-57	Listeria monocytogenes	95.98	unclassified	0.70	Salmonella enterica	0.06	Listeria innocua	0.04	✔
OFN-61	Listeria monocytogenes	95.43	unclassified	0.66	Listeria innocua	0.14	Salmonella enterica	0.09	✔
OFN-55	Listeria monocytogenes	94.74	unclassified	1.33	Listeria innocua	0.19	Salmonella enterica	0.06	✔
OFN-62	Listeria monocytogenes	94.50	unclassified	1.38	Listeria innocua	0.20	Salmonella enterica	0.12	✔
OFN-60	Listeria monocytogenes	94.88	unclassified	0.91	Listeria innocua	0.19	Salmonella enterica	0.06	✔
OFN-58	Listeria monocytogenes	94.00	unclassified	1.03	Listeria innocua	0.30	Salmonella enterica	0.19	✔
OFN-01	Listeria monocytogenes	93.90	unclassified	1.20	Listeria innocua	0.51	Listeria phage LP-101	0.04	✔
OFN-04	Listeria monocytogenes	94.43	unclassified	0.71	Listeria innocua	0.27	Listeria phage LP-101	0.03	✔
OFN-59	Listeria monocytogenes	95.20	unclassified	0.92	Listeria innocua	0.17	Salmonella enterica	0.09	✔
OFN-64	Listeria monocytogenes	95.63	unclassified	0.84	Listeria innocua	0.18	Listeria phage LP-101	0.02	✔
OFN-65	Listeria monocytogenes	95.55	unclassified	1.01	Listeria innocua	0.26	Lactococcus lactis	0.03	✔
OFN-56	Listeria monocytogenes	95.08	unclassified	0.80	Listeria innocua	0.19	Salmonella enterica	0.05	✔
OFN-68	Listeria monocytogenes	95.75	unclassified	0.94	Listeria innocua	0.19	Listeria phage LP-101	0.03	✔
OFN-67	Listeria monocytogenes	95.43	unclassified	0.94	Listeria innocua	0.25	Lactococcus lactis	0.02	✔
OFN-66	Listeria monocytogenes	95.61	unclassified	0.87	Listeria innocua	0.24	Lactococcus lactis	0.02	✔
OFN-03	Listeria monocytogenes	89.80	Listeria innocua	4.37	unclassified	0.93	Listeria welshimeri	0.03	✔
OFN-63	Listeria monocytogenes	95.98	unclassified	0.68	Listeria innocua	0.20	Salmonella enterica	0.02	✔
OFN-02	Listeria monocytogenes	89.99	unclassified	4.37	Lactococcus lactis	0.64	Listeria innocua	0.55	✔

☰

• Report summary
• Sequence data
• Species identification
• MLST
• Serotyping
• Resistome
• Assembly and annotation
• Reference genome
• Core genome
• Core SNP phylogeny
• Pairwise core SNP distances
• Core SNP density
• Pan genome
• Software versions
• About

MLST ▲

Download: ⬇mlst.csv

Isolate	Scheme	Sequence Type	Allele	Allele	Allele	Allele	Allele	Allele	Allele	Quality
OFN-01	lmonocytogenes	5	abcZ(2)	bglA(1)	cat(11)	dapE(3)	dat(3)	ldh(1)	lhkA(7)	✔
OFN-02	lmonocytogenes	5	abcZ(2)	bglA(1)	cat(11)	dapE(3)	dat(3)	ldh(1)	lhkA(7)	✔
OFN-03	lmonocytogenes	-	abcZ(2)	bglA(1)	cat(11,83)	dapE(3)	dat(3,20)	ldh(9?)	lhkA(7)	✘
OFN-04	lmonocytogenes	5	abcZ(2)	bglA(1)	cat(11)	dapE(3)	dat(3)	ldh(1)	lhkA(7)	✔
OFN-55	lmonocytogenes	5	abcZ(2)	bglA(1)	cat(11)	dapE(3)	dat(3)	ldh(1)	lhkA(7)	✔
OFN-56	lmonocytogenes	-	abcZ(2)	bglA(9?)	cat(11)	dapE(3)	dat(3)	ldh(1)	lhkA(7)	✘
OFN-57	lmonocytogenes	5	abcZ(2)	bglA(1)	cat(11)	dapE(3)	dat(3)	ldh(1)	lhkA(7)	✔
OFN-58	lmonocytogenes	5	abcZ(2)	bglA(1)	cat(11)	dapE(3)	dat(3)	ldh(1)	lhkA(7)	✔
OFN-59	lmonocytogenes	5	abcZ(2)	bglA(1)	cat(11)	dapE(3)	dat(3)	ldh(1)	lhkA(7)	✔
OFN-60	lmonocytogenes	5	abcZ(2)	bglA(1)	cat(11)	dapE(3)	dat(3)	ldh(1)	lhkA(7)	✔
OFN-61	lmonocytogenes	5	abcZ(2)	bglA(1)	cat(11)	dapE(3)	dat(3)	ldh(1)	lhkA(7)	✔
OFN-62	lmonocytogenes	5	abcZ(2)	bglA(1)	cat(11)	dapE(3)	dat(3)	ldh(1)	lhkA(7)	✔
OFN-63	lmonocytogenes	5	abcZ(2)	bglA(1)	cat(11)	dapE(3)	dat(3)	ldh(1)	lhkA(7)	✔
OFN-64	lmonocytogenes	5	abcZ(2)	bglA(1)	cat(11)	dapE(3)	dat(3)	ldh(1)	lhkA(7)	✔
OFN-65	lmonocytogenes	5	abcZ(2)	bglA(1)	cat(11)	dapE(3)	dat(3)	ldh(1)	lhkA(7)	✔
OFN-66	lmonocytogenes	5	abcZ(2)	bglA(1)	cat(11)	dapE(3)	dat(3)	ldh(1)	lhkA(7)	✔
OFN-67	lmonocytogenes	5	abcZ(2)	bglA(1)	cat(11)	dapE(3)	dat(3)	ldh(1)	lhkA(7)	✔
OFN-68	lmonocytogenes	5	abcZ(2)	bglA(1)	cat(11)	dapE(3)	dat(3)	ldh(1)	lhkA(7)	✔

☰

• Report summary
• Sequence data
• Species identification
• MLST
• Serotyping
• Resistome
• Assembly and annotation
• Reference genome
• Core genome
• Core SNP phylogeny
• Pairwise core SNP distances
• Core SNP density
• Pan genome
• Software versions
• About

Serotyping ▲

Download: ⬇serotype.csv

Isolate	isSEROTYPE	AMPLICONS	Quality
OFN-01	1/2b,3b,7	ORF2819,Prs	✔
OFN-02	1/2b,3b,7	ORF2819,Prs	✔
OFN-03	-	-	✘
OFN-04	1/2b,3b,7	ORF2819,Prs	✔
OFN-55	1/2b,3b,7	ORF2819,Prs	✔
OFN-56	1/2b,3b,7	ORF2819,Prs	✔
OFN-57	1/2b,3b,7	ORF2819,Prs	✔
OFN-58	1/2b,3b,7	ORF2819,Prs	✔
OFN-59	1/2b,3b,7	ORF2819,Prs	✔
OFN-60	1/2b,3b,7	ORF2819,Prs	✔
OFN-61	1/2b,3b,7	ORF2819,Prs	✔
OFN-62	1/2b,3b,7	ORF2819,Prs	✔
OFN-63	1/2b,3b,7	ORF2819,Prs	✔
OFN-64	1/2b,3b,7	ORF2819,Prs	✔
OFN-65	1/2b,3b,7	ORF2819,Prs	✔
OFN-66	1/2b,3b,7	ORF2819,Prs	✔
OFN-67	1/2b,3b,7	ORF2819,Prs	✔
OFN-68	1/2b,3b,7	ORF2819,Prs	✔

☰

• Report summary
• Sequence data
• Species identification
• MLST
• Serotyping
• Resistome
• Assembly and annotation
• Reference genome
• Core genome
• Core SNP phylogeny
• Pairwise core SNP distances
• Core SNP density
• Pan genome
• Software versions
• About

Resistome ▲

Download: ⬇resistome.csv

Isolate	Found
OFN-57	0
OFN-61	0
OFN-55	0
OFN-62	0
OFN-60	0
OFN-58	0
OFN-01	0
OFN-04	0
OFN-59	0
OFN-64	0
OFN-65	0
OFN-56	0
OFN-68	0
OFN-67	0
OFN-66	0
OFN-03	0
OFN-63	0
OFN-02	0

☰

• Report summary
• Sequence data
• Species identification
• MLST
• Serotyping
• Resistome
• Assembly and annotation
• Reference genome
• Core genome
• Core SNP phylogeny
• Pairwise core SNP distances
• Core SNP density
• Pan genome
• Software versions
• About

Assembly and annotation ▲

Download: ⬇assembly.csv

Isolate	Contigs	bp	ok	Ns	gaps	min	avg	max	N50	Insert size (25,50,75)%	CDS	rRNA	tRNA	tmRNA	Quality
OFN-01	118	3079295	3079295	0	0	503	26095	311920	63596	(356, 491, 624)	3027	2	45	1	✔
OFN-02	104	3076915	3076915	0	0	500	29585	296665	97924	(356, 488, 618)	3018	2	47	1	✔
OFN-03	2074	5661956	5661956	0	0	500	2729	47421	4354	(207, 273, 361)	5287	3	39		✘
OFN-04	775	2944028	2944028	0	0	500	3798	31893	6271	(214, 282, 369)	2790		27	1	✘
OFN-55	506	3334287	3334287	0	0	500	6589	293410	100195	(299, 397, 507)	3181	6	48	1	✘
OFN-56	114	3006358	3006358	0	0	517	26371	248174	54113	(271, 369, 480)	2941		44	1	✔
OFN-57	67	2957057	2957057	0	0	503	44135	324634	123016	(290, 394, 509)	2900	1	46	1	✔
OFN-58	82	3014361	3014361	0	0	510	36760	251137	115046	(335, 460, 580)	2959	3	42	1	✔
OFN-59	61	3004754	3004754	0	0	566	49258	439136	135564	(290, 397, 510)	2948	2	48	1	✔
OFN-60	75	3006879	3006879	0	0	503	40091	397472	102259	(256, 349, 458)	2952	2	47	1	✔
OFN-61	65	3004441	3004441	0	0	532	46222	595023	126896	(270, 356, 465)	2951	2	44	1	✔
OFN-62	43	3005219	3005219	0	0	543	69888	595503	176104	(299, 438, 562)	2952	2	47	1	✔
OFN-63	53	3005659	3005659	0	0	527	56710	447525	164693	(356, 480, 609)	2949	2	47	1	✔
OFN-64	74	3006500	3006500	0	0	548	40628	401333	97924	(345, 478, 605)	2949	2	47	1	✔
OFN-65	42	3008500	3008500	0	0	540	71630	595568	293255	(322, 449, 575)	2955	3	47	1	✔
OFN-66	62	3006054	3006054	0	0	515	48484	308846	155920	(327, 453, 581)	2950	2	47	1	✔
OFN-67	53	3004568	3004568	0	0	526	56689	469587	124208	(327, 457, 586)	2951	2	47	1	✔
OFN-68	47	3005256	3005256	0	0	503	63941	475435	170229	(330, 458, 584)	2954	3	53	1	✔

☰

• Report summary
• Sequence data
• Species identification
• MLST
• Serotyping
• Resistome
• Assembly and annotation
• Reference genome
• Core genome
• Core SNP phylogeny
• Pairwise core SNP distances
• Core SNP density
• Pan genome
• Software versions
• About

Reference genome ▲

Download: ⬇reference.csv

Sequence	Length	Description
CP011398	3039897	Listeria monocytogenes strain CFSAN008100, complete genome.
CP011399	68224	Listeria monocytogenes strain CFSAN008100 plasmid pCFSAN008100, complete sequence.
TOTAL	3108121	Total reference size in bp

☰

• Report summary
• Sequence data
• Species identification
• MLST
• Serotyping
• Resistome
• Assembly and annotation
• Reference genome
• Core genome
• Core SNP phylogeny
• Pairwise core SNP distances
• Core SNP density
• Pan genome
• Software versions
• About

Core genome ▲

Download: ⬇core.csv

Isolate	Aligned Bases	Reference bases	% Aligned Bases	Quality
OFN-01	2922354	3108121	94.02	✔
OFN-02	2921293	3108121	93.99	✔
OFN-03	2951391	3108121	94.96	✔
OFN-04	2926110	3108121	94.14	✔
OFN-55	2924614	3108121	94.10	✔
OFN-56	2925058	3108121	94.11	✔
OFN-57	2898554	3108121	93.26	✔
OFN-58	2369028	3108121	76.22	?
OFN-59	2924415	3108121	94.09	✔
OFN-60	2924971	3108121	94.11	✔
OFN-61	2924856	3108121	94.10	✔
OFN-62	2921905	3108121	94.01	✔
OFN-63	2923076	3108121	94.05	✔
OFN-64	2922762	3108121	94.04	✔
OFN-65	2919225	3108121	93.92	✔
OFN-66	2922977	3108121	94.04	✔
OFN-67	2919816	3108121	93.94	✔
OFN-68	2922597	3108121	94.03	✔
AVERAGE	2892500	3108121	93.06	✔

☰

• Report summary
• Sequence data
• Species identification
• MLST
• Serotyping
• Resistome
• Assembly and annotation
• Reference genome
• Core genome
• Core SNP phylogeny
• Pairwise core SNP distances
• Core SNP density
• Pan genome
• Software versions
• About

Core SNP phylogeny ▲

Download: ⬇core.aln ⬇tree.newick

Core SNP alignment has 18 taxa and 1149 bp.

☰

• Report summary
• Sequence data
• Species identification
• MLST
• Serotyping
• Resistome
• Assembly and annotation
• Reference genome
• Core genome
• Core SNP phylogeny
• Pairwise core SNP distances
• Core SNP density
• Pan genome
• Software versions
• About

Pairwise core SNP distances ▲

Download: ⬇snpdist.csv

ID	OFN-01	OFN-02	OFN-03	OFN-04	OFN-55	OFN-56	OFN-57	OFN-58	OFN-59	OFN-60	OFN-61	OFN-62	OFN-63	OFN-64	OFN-65	OFN-66	OFN-67	OFN-68	Reference
OFN-01	0	16	723	736	733	736	735	704	733	733	734	727	734	733	735	733	736	733	697
OFN-02	16	0	715	728	725	728	727	696	725	725	726	719	726	725	727	725	728	725	689
OFN-03	723	715	0	25	22	25	24	159	22	22	23	16	23	22	24	22	25	22	802
OFN-04	736	728	25	0	5	8	7	160	5	5	6	13	6	5	7	5	8	5	827
OFN-55	733	725	22	5	0	5	4	157	2	2	3	10	3	2	4	2	5	2	824
OFN-56	736	728	25	8	5	0	7	160	5	5	6	13	6	5	7	5	8	5	827
OFN-57	735	727	24	7	4	7	0	157	4	4	5	12	5	4	6	4	7	4	826
OFN-58	704	696	159	160	157	160	157	0	157	157	158	151	158	157	159	157	160	157	671
OFN-59	733	725	22	5	2	5	4	157	0	2	3	10	3	2	4	2	5	2	824
OFN-60	733	725	22	5	2	5	4	157	2	0	3	10	3	2	4	2	5	2	824
OFN-61	734	726	23	6	3	6	5	158	3	3	0	11	4	3	5	3	6	3	825
OFN-62	727	719	16	13	10	13	12	151	10	10	11	0	11	10	12	10	13	10	818
OFN-63	734	726	23	6	3	6	5	158	3	3	4	11	0	3	5	1	6	1	825
OFN-64	733	725	22	5	2	5	4	157	2	2	3	10	3	0	4	2	5	2	824
OFN-65	735	727	24	7	4	7	6	159	4	4	5	12	5	4	0	4	7	4	826
OFN-66	733	725	22	5	2	5	4	157	2	2	3	10	1	2	4	0	5	0	824
OFN-67	736	728	25	8	5	8	7	160	5	5	6	13	6	5	7	5	0	5	827
OFN-68	733	725	22	5	2	5	4	157	2	2	3	10	1	2	4	0	5	0	824
Reference	697	689	802	827	824	827	826	671	824	824	825	818	825	824	826	824	827	824	0

☰

• Report summary
• Sequence data
• Species identification
• MLST
• Serotyping
• Resistome
• Assembly and annotation
• Reference genome
• Core genome
• Core SNP phylogeny
• Pairwise core SNP distances
• Core SNP density
• Pan genome
• Software versions
• About

Core SNP density ▲

☰

• Report summary
• Sequence data
• Species identification
• MLST
• Serotyping
• Resistome
• Assembly and annotation
• Reference genome
• Core genome
• Core SNP phylogeny
• Pairwise core SNP distances
• Core SNP density
• Pan genome
• Software versions
• About

Pan genome ▲

Download: ⬇pan.csv

Ortholog class	Definition	Count
Core genes	(99% <= strains <= 100%)	2154
Soft core genes	(95% <= strains < 99%)	0
Shell genes	(15% <= strains < 95%)	832
Cloud genes	(0% <= strains < 15%)	3173
Total genes	(0% <= strains <= 100%)	6159

☰

• Report summary
• Sequence data
• Species identification
• MLST
• Serotyping
• Resistome
• Assembly and annotation
• Reference genome
• Core genome
• Core SNP phylogeny
• Pairwise core SNP distances
• Core SNP density
• Pan genome
• Software versions
• About

Software versions ▲

Download: ⬇tools.csv

Tool	Version
Abricate	0.3
BWA MEM	0.7.13-r1126
FastTree	2.1.8 Double precision (No SSE3), OpenMP (8 threads):
FreeBayes	1.0.2-dirty
Kraken	0.10.5-beta
MLST	2.6
MegaHit	1.0.3
Newick-Utils	(unable to determine version)
Nullarbor	1.20
Prokka	1.12-beta
Roary	6.2
SAMtools	1.3
SPAdes	3.8.0
Snippy	3.1
Trimmomatic	(unable to determine version)

☰

• Report summary
• Sequence data
• Species identification
• MLST
• Serotyping
• Resistome
• Assembly and annotation
• Reference genome
• Core genome
• Core SNP phylogeny
• Pairwise core SNP distances
• Core SNP density
• Pan genome
• Software versions
• About

About ▲

• This primary author of Nullarbor is Torsten Seemann.
• You can download the software from Github.
• Please report bugs at the Nullarbor Issue Tracker.
• If you use Nullarbor please use the latest citation.