plasmidfinder

plasmidfinder

About: |

Identifies plasmids in total or partial sequenced isolates of bacteria.

Documentation : https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/

Citation : https://pubmed.ncbi.nlm.nih.gov/24777092/

Directory tree:

plasmidfinder/
├── plasmidfinder_result.tsv
├── sample
│   ├── data.json
│   ├── Hit_in_genome_seq.fsa
│   ├── Plasmid_seqs.fsa
│   ├── results_tab.tsv
│   ├── results.txt
│   └── tmp
│       ├── out_enterobacteriaceae.xml
│       ├── out_Inc18.xml
│       ├── out_NT_Rep.xml
│       ├── out_Rep1.xml
│       ├── out_Rep2.xml
│       ├── out_Rep3.xml
│       ├── out_RepA_N.xml
│       ├── out_RepL.xml
│       └── out_Rep_trans.xml
└── sample_plasmidfinder.tsv

Example file for an individual sample (sample/data.json)

{"plasmidfinder": {"user_input": {"method": "blast", "filename(s)": ["Acinetobacter_GCF_008632635.1.fasta"], "file_format": "fasta"}, "run_info": {"date": "02.02.2024", "time": "18:22:58"}, "results": {"Enterobacteriaceae": {"enterobacteriaceae": "No hit found"}, "Gram Positive": {"Rep2": "No hit found", "RepL": "No hit found", "NT_Rep": "No hit found", "Inc18": "No hit found", "Rep1": "No hit found", "Rep_trans": "No hit found", "RepA_N": "No hit found", "Rep3": "No hit found"}}}}

Example file for a run (plasmidfinder_results.tsv)

sample	Database	Plasmid	Identity	Query / Template length	Contig	Position in contig	Note	Accession number
cronobacter_GCF_001277215.2	enterobacteriaceae	IncFIB(pCTU1)	91.1	809 / 809	NZ_CP013941.1 Cronobacter malonaticus LMG 23826 plasmid pCMA1, complete sequence	22368..23176	pCTU1	FN543094
cronobacter_GCF_001277215.2	enterobacteriaceae	IncFIB(pCTU3)	99.28	693 / 693	NZ_CP013942.1 Cronobacter malonaticus LMG 23826 plasmid pCMA2, complete sequence	2185..2875	pCTU3	FN543096
ecoli_GCA_003019175.1	enterobacteriaceae	IncB/O/K/Z	99.34	152 / 152	CP027547.1 Escherichia coli strain 2013C-4187 plasmid unnamed, complete sequence	62513..62664		GQ259888
ecoli_GCA_003019175.1	enterobacteriaceae	IncFIB(AP001918)	96.92	682 / 682	CP027547.1 Escherichia coli strain 2013C-4187 plasmid unnamed, complete sequence	33797..34478		AP001918
ecoli_GCA_009738455.1	enterobacteriaceae	IncFIA	99.25	268 / 388	CP046526.1 Escherichia coli strain RM19259 plasmid pRM19259, complete sequence	19012..19279		AP001918
ecoli_GCA_009738455.1	enterobacteriaceae	IncFIB(AP001918)	98.24	682 / 682	CP046526.1 Escherichia coli strain RM19259 plasmid pRM19259, complete sequence	11410..12091		AP001918
ecoli_GCA_009738455.1	enterobacteriaceae	IncFII	96.17	261 / 261	CP046526.1 Escherichia coli strain RM19259 plasmid pRM19259, complete sequence	57187..57445		AY458016
ecoli_GCA_023823105.1	enterobacteriaceae	IncB/O/K/Z	100.0	151 / 151	CP090404.1 Shigella sp. PIB plasmid pPIB-2, complete sequence	13693..13843		CU928147
ecoli_GCA_023823105.1	enterobacteriaceae	IncFII(29)	96.93	261 / 259	CP090406.1 Shigella sp. PIB plasmid pPIB-4, complete sequence	2809..3068	pUTI89	CP003035
ecoli_GCA_023823105.1	enterobacteriaceae	IncI1	100.0	142 / 142	CP090403.1 Shigella sp. PIB plasmid pPIB-1, complete sequence	82421..82562	Alpha	AP005147
ecoli_GCA_023823105.1	enterobacteriaceae	IncI2	99.38	324 / 324	CP090405.1 Shigella sp. PIB plasmid pPIB-3, complete sequence	35294..35617		KP347127
kleb_GCF_000240185.1	enterobacteriaceae	Col(KPHS6)	100.0	178 / 178	NC_016841.1 Klebsiella pneumoniae subsp. pneumoniae HS11286 plasmid pKPHS6, complete sequence	326..503		NC016841
kleb_GCF_000240185.1	enterobacteriaceae	Col156	94.81	154 / 154	NC_016840.1 Klebsiella pneumoniae subsp. pneumoniae HS11286 plasmid pKPHS4, complete sequence	3143..3296		NC009781
kleb_GCF_000240185.1	enterobacteriaceae	IncA/C2	100.0	417 / 417	NC_016839.1 Klebsiella pneumoniae subsp. pneumoniae HS11286 plasmid pKPHS3, complete sequence	104196..104612		JN157804
kleb_GCF_000240185.1	enterobacteriaceae	IncFIB(pKPHS1)	100.0	560 / 560	NC_016838.1 Klebsiella pneumoniae subsp. pneumoniae HS11286 plasmid pKPHS1, complete sequence	201..760	pKPHS1	CP003223
kleb_GCF_000240185.1	enterobacteriaceae	IncFII(K)	98.65	148 / 148	NC_016846.1 Klebsiella pneumoniae subsp. pneumoniae HS11286 plasmid pKPHS2, complete sequence	39090..39237		CP000648
kleb_GCF_000240185.1	enterobacteriaceae	IncR	99.2	251 / 251	NC_016846.1 Klebsiella pneumoniae subsp. pneumoniae HS11286 plasmid pKPHS2, complete sequence	110833..111083		DQ449578
kleb_GCF_015139575.1	enterobacteriaceae	IncI1	99.3	142 / 142	NZ_AP022548.1 Klebsiella michiganensis strain THO-011 plasmid pTHO-011-1, complete sequence	47228..47369	Alpha	AP005147
salm_GCA_001652385.2	enterobacteriaceae	IncFIB(S)	99.84	643 / 643	CP075142.1 Salmonella enterica strain CFSAN033950 plasmid pCFSAN033950, complete sequence	50813..51455		FN432031
salm_GCA_001652385.2	enterobacteriaceae	IncFII(S)	97.71	262 / 262	CP075142.1 Salmonella enterica strain CFSAN033950 plasmid pCFSAN033950, complete sequence	33331..33590		CP000858
salm_GCA_013344545.1	enterobacteriaceae	IncFIA(HI1)	100.0	388 / 388	AP020333.1 Salmonella enterica SESen3709 plasmid pSESen3709_1 DNA, complete genome	76201..76588	HI1	AF250878
salm_GCA_013344545.1	enterobacteriaceae	IncHI1A	100.0	420 / 420	AP020333.1 Salmonella enterica SESen3709 plasmid pSESen3709_1 DNA, complete genome	13993..14412		AF250878
salm_GCA_013344545.1	enterobacteriaceae	IncHI1B(R27)	100.0	540 / 540	AP020333.1 Salmonella enterica SESen3709 plasmid pSESen3709_1 DNA, complete genome	377..916	R27	AF250878
salm_GCA_019710395.3	enterobacteriaceae	IncFII(pCoo)	97.68	259 / 262	CP081190.2 Salmonella enterica strain sg1722-2 plasmid unnamed1, complete sequence	84626..84884	pCoo	CR942285
strep1_GCA_001412635.1	Rep_trans	repUS43	99.83	1206 / 1206	CP012805.1 Streptococcus anginosus strain J4211, complete genome	254264..255469	CDS12738(DOp1)	CP003584
strep1_GCA_016724885.1	Rep2	rep34	91.03	602 / 633	CP068058.1 Streptococcus dysgalactiae strain FDAARGOS_1157 plasmid unnamed1, complete sequence	949..1547	repB(pA852)	KC895878
strep1_GCA_016724885.1	Rep1	repUS61	99.79	942 / 942	CP068058.1 Streptococcus dysgalactiae strain FDAARGOS_1157 plasmid unnamed1, complete sequence	4559..5500	repA(pA996)	KC895877
strep1_GCA_016724885.1	Rep1	repUS62	99.7	1005 / 1005	CP068059.1 Streptococcus dysgalactiae strain FDAARGOS_1157 plasmid unnamed2, complete sequence	897..1901	repA(pDN571)	AY648561
streppneumo_GCA_000221985.1	Rep3	repUS37	100.0	810 / 810	CP002926.1 Streptococcus pseudopneumoniae IS7493 plasmid pDRPIS7493, complete sequence	2203..3012	SPPN11498(pDRPIS7493)	CP002926
streppneumo_GCA_000221985.1	Rep_trans	repUS43	100.0	1206 / 1206	CP002925.1 Streptococcus pseudopneumoniae IS7493, complete genome	226996..228201	CDS12738(DOp1)	CP003584
streppneumo_GCA_002076835.1	Rep1	rep13	100.0	846 / 846	CP020549.1 Streptococcus pneumoniae strain Hu17 chromosome, partial sequence	1116628..1117473	rep(pKH13)	EU170347
streppneumo_GCA_002076835.1	Rep_trans	repUS43	100.0	1203 / 1206	CP020549.1 Streptococcus pneumoniae strain Hu17 chromosome, partial sequence	1258053..1259255	CDS12738(DOp1)	CP003584