Dear all,

a) below is the result for typing the plasmid sample unsing Kmerid
(https://github.com/phe-bioinformatics/kmerid).

b) is a resistance gene test using SRST2
(https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0090-6
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs)
with the ARG-ANNOT db
(Gupta et al, Antimicrob Agents Chemother 2014; 58(1):212. DOI: [10.1128/AAC.01310-13](http://aac.asm.org/content/58/1/212.abstract)

c) is a gene test using the Plasmidfinder-DB

d)
An inital assembly has been generated, with the following stats:
Longest sequence length  :          29033 bp
N50:	1840	(686 sequences)	(2227742 bp combined)
The contigs are at
http://genomics-lab.fleming.gr/fleming/external/klpn/plasmid1/a.lines.fasta
The use of other error-tolerant assemblers is under investigation.

Detailed results are at:
http://genomics-lab.fleming.gr/fleming/external/klpn/plasmid1

BW
Martin

a)
#Kmer based similarities
#similarity	groups	file
94.172722	escherichia	Escherichia_coli_K_12_substr__W3110_uid161931.fa
67.702538	escherichia	Escherichia_coli_W_uid162011.fa
56.832306	escherichia	Escherichia_coli_O157_H7_TW14359_uid59235.fa
54.505398	escherichia	Escherichia_coli_IAI39_uid59381.fa
52.853363	escherichia	Escherichia_coli_SMS_3_5_uid58919.fa
52.828918	escherichia	Escherichia_coli_042_uid161985.fa
50.437317	escherichia	Escherichia_coli_NA114_uid162139.fa
49.821507	escherichia	Escherichia_coli_O127_H6_E2348_69_uid59343.fa
49.435032	escherichia	Escherichia_coli_UM146_uid162043.fa
24.549402	escherichia	Escherichia_fergusonii_ATCC_35469_uid59375.fa
4.362907	salmonella	Salmonella_enterica_serovar_Paratyphi_A_ATCC_9150_uid58201.fa
4.300567	salmonella	Salmonella_enterica_serovar_Javiana_CFSAN001992_uid190101.fa
4.296291	salmonella	Salmonella_enterica_serovar_Gallinarum_pullorum_RKS5078_uid87035.fa
4.220073	salmonella	Salmonella_enterica_serovar_Agona_SL483_uid59431.fa
4.209170	salmonella	Salmonella_enterica_serovar_Choleraesuis_SC_B67_uid58017.fa
4.171369	salmonella	Salmonella_enterica_serovar_Typhi_Ty2_uid57973.fa
4.156878	salmonella	Salmonella_enterica_serovar_Typhimurium_UK_1_uid87049.fa
4.075833	salmonella	Salmonella_enterica_Serovar_Cubana_CFSAN002050_uid212973.fa
3.959964	salmonella	Salmonella_enterica_arizonae_serovar_62_z4_z23__uid58191.fa
3.945707	salmonella	Salmonella_bongori_NCTC_12419_uid70155.fa

b)
#fullgenes
Sample	DB	gene	allele	coverage	depth	diffs	uncertainty	divergence	length	maxMAF	clusterid	seqid	annotation
R_2017_12_07_15_50_07_user_IONAS-374-KELPNO_171207.KLPNC4-trf5504p.IonXpress_017	PlasmidFinder	Col	_Col-plasmid_1_J01566__22	98.881	14.295	24snp2indel2holes		9.023	268	0.375	138	_22	

#genes
Sample	DB	gene	allele	coverage	depth	diffs	uncertainty	divergence	length	maxMAF	clusterid	seqid	annotation
R_2017_12_07_15_50_07_user_IONAS-374-KELPNO_171207.KLPNC4-trf5504p.IonXpress_017	ARGannot_r2	TEM-1D_Bla	TEM-171_1017	100.0	175.988			0.0	861	0.227	205	1017	no;no;TEM-171;Bla;GQ149347;5270-6130;861
R_2017_12_07_15_50_07_user_IONAS-374-KELPNO_171207.KLPNC4-trf5504p.IonXpress_017	ARGannot_r2	MrdA_Bla	MrdA_836	99.947	110.552	1indel		0.0	1902	0.342	16	836	no;no;MrdA;Bla;CP002291;666340-664439;1902
R_2017_12_07_15_50_07_user_IONAS-374-KELPNO_171207.KLPNC4-trf5504p.IonXpress_017	ARGannot_r2	AmpC1_Ecoli_Bla	AmpC1_1670	100.0	120.098			0.0	1305	0.383	49	1670	no;no;AmpC1;Bla;FN649414;2765051-2766355;1305
R_2017_12_07_15_50_07_user_IONAS-374-KELPNO_171207.KLPNC4-trf5504p.IonXpress_017	ARGannot_r2	AacAad_AGly	Aac6-Ib_1677	100.0	7331.832			0.0	606	0.11	43	1677	no;no;Aac6-Ib;AGly;NC_015515;3943-4548;606
R_2017_12_07_15_50_07_user_IONAS-374-KELPNO_171207.KLPNC4-trf5504p.IonXpress_017	ARGannot_r2	AmpC2_Ecoli_Bla	AmpC2_346	100.0	122.745			0.0	1134	0.197	99	346	no;no;AmpC2;Bla;CP002970;332756-333889;1134
R_2017_12_07_15_50_07_user_IONAS-374-KELPNO_171207.KLPNC4-trf5504p.IonXpress_017	ARGannot_r2	AMPH_Ecoli_Bla	AMPH_615	100.0	109.19			0.0	1158	0.429	89	615	no;no;AMPH;Bla;AP012030;395554-396711;1158
R_2017_12_07_15_50_07_user_IONAS-374-KELPNO_171207.KLPNC4-trf5504p.IonXpress_017	ARGannot_r2	NDM-1_Bla	NDM-1_1220	100.0	7022.391			0.0	813	0.448	257	1220	no;no;NDM-1;Bla;KR091911;68724-67912;813

c)
#fullgenes
Sample	DB	gene	allele	coverage	depth	diffs	uncertainty	divergence	length	maxMAF	clusterid	seqid	annotation
R_2017_12_07_15_50_07_user_IONAS-374-KELPNO_171207.KLPNC4-trf5504p.IonXpress_017	PlasmidFinder	Col	_Col-plasmid_1_J01566__22	98.881	14.295	24snp2indel2holes		9.023	268	0.375	138	_22	

#genes
Sample	Col
R_2017_12_07_15_50_07_user_IONAS-374-KELPNO_171207.KLPNC4-trf5504p.IonXpress_017	_Col-plasmid_1_J01566__22*