Clostridium perfringens: Difference between revisions

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Summary:
  ~ 10 strains in NCBI Taxonomy
  8 genome projects
  2 complete genomes
  7 assemblies in NCBI AA (all TIGR/JCVI)
  7 trace sets (all TIGR/JCVI)
== Data sources ==
== Data sources ==


'''NCBI:'''  
'''NCBI:'''  
* [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1502 Tax Browser]
* [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1502 Tax Browser]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=12308 Genome Projects]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=Clostridium%perfringens Genome Projects]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=Clostridium%perfringens Genome Projects]
* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/ NCBI_TA_FTP]
* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/ NCBI_TA_FTP]
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Strains:
Strains:
   1. A: not sequenced  
   1. A: not sequenced  
   2. ATCC 13124: JCVI; 54K reads, 1 contig ; finished; 3,256,683 bp ;28.38% GC ; ??? what about plasmids
   2. ATCC 13124: JCVI; 54K reads, 1 contig ; finished; 3,256,683 bp ;28.38% GC ; ??? what about plasmids ; uploaded to Insignia
   3. B str. ATCC 3626: JCVI, 38K reads, 98 contigs
   3. B str. ATCC 3626: JCVI, 38K reads, 98 contigs
   4. C str. JGS1495: JCVI, 40K reads, 84 contigs
   4. C str. JGS1495: JCVI, 40K reads, 84 contigs
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   7. E str. JGS1987: JCVI, 38K reads, 101 contigs
   7. E str. JGS1987: JCVI, 38K reads, 101 contigs
   8. NCTC 8239: JCVI, 38K reads, 55 contigs
   8. NCTC 8239: JCVI, 38K reads, 55 contigs
   9. SM101: JCVI+TIGR, 43K reads, 3 contigs (chromosome+2 plasmids) (finished)
   9. SM101: JCVI+TIGR, 43K reads, 3 contigs (chromosome+2 plasmids) (finished) ; uploaded to Insignia
  10. 13: University of Tsukuba Japan, 52K reads (not available in NCBI TA), 2 contigs(chomosome+plasmid), phrap assembly (finished);  
  10. 13: University of Tsukuba Japan, 52K reads (not available in NCBI TA), 2 contigs(chomosome+plasmid), phrap assembly (finished); uploaded to Insignia
     password protected web site : http://kantaro2.grt.kyushu-u.ac.jp/microb/welch/
     password protected web site : http://kantaro2.grt.kyushu-u.ac.jp/microb/welch/


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* [[Media:C_perfringens.AA.qc.combine|qc stats]]
* [[Media:C_perfringens.AA.qc.combine|qc stats]]
ATCC_13124 : many missoriented reads


CBCB CA3 assemblies:
CBCB CA3 assemblies:
                     Placed  Deg  Total
                     Placed  Deg  Total
   1. A
   1. A
   2. ATCC_13124        37  69  106       
   2. ATCC_13124        37  69  106       
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   FINISHING  2994
   FINISHING  2994
   Total      543810
   Total      543810
== Insignia uploads ==
Assemblies selected:
    /fs/szasmg2/Bacteria/C_perfringens/ATCC_13124/best -> AA/CS--AI-1565/
    /fs/szasmg2/Bacteria/C_perfringens/B_str__ATCC_3626/best ->    AA/CS--AI-2899/
    /fs/szasmg2/Bacteria/C_perfringens/CPE_str__F4969/best -> 2007_1005_WGA/
    /fs/szasmg2/Bacteria/C_perfringens/C_str__JGS1495/best ->    AA/CS--AI-2889/
    /fs/szasmg2/Bacteria/C_perfringens/E_str__JGS1987/best -> 2007_1005_WGA
    /fs/szasmg2/Bacteria/C_perfringens/SM101/best -> AA/CS--AI-1688/
    /fs/szasmg2/Bacteria/C_perfringens/str__nctc8239/best -> 2007_1005_WGA/

Latest revision as of 17:56, 19 August 2008

Summary: 

 ~ 10 strains in NCBI Taxonomy
 8 genome projects
 2 complete genomes
 7 assemblies in NCBI AA (all TIGR/JCVI)
 7 trace sets (all TIGR/JCVI)

Data sources

NCBI:

Strains: 

 1. A: not sequenced 
 2. ATCC 13124: JCVI; 54K reads, 1 contig ; finished; 3,256,683 bp ;28.38% GC ; ??? what about plasmids ; uploaded to Insignia
 3. B str. ATCC 3626: JCVI, 38K reads, 98 contigs
 4. C str. JGS1495: JCVI, 40K reads, 84 contigs
 5. CPE str. F4969: JCVI, 37K reads, 74 contig
 6. D: not sequenced 
 7. E str. JGS1987: JCVI, 38K reads, 101 contigs
 8. NCTC 8239: JCVI, 38K reads, 55 contigs
 9. SM101: JCVI+TIGR, 43K reads, 3 contigs (chromosome+2 plasmids) (finished) ; uploaded to Insignia
10. 13: University of Tsukuba Japan, 52K reads (not available in NCBI TA), 2 contigs(chomosome+plasmid), phrap assembly (finished); uploaded to Insignia
    password protected web site : http://kantaro2.grt.kyushu-u.ac.jp/microb/welch/

File locations: 

 /fs/szasmg2/Bacteria/C_perfringens

NCBI AA assemblied:

ATCC_13124 : many missoriented reads

CBCB CA3 assemblies: 

                    Placed  Deg  Total  
 1. A
 2. ATCC_13124         37   69   106      
 3. B_str__ATCC_362    64   65   129
 4. C_str__JGS1495     53   39    92 
 5. CPE_str__F4969     60    4    64     better
 6. D
 7. E_str__JGS1987     78   15    83     better
 8. str__nctc8239      48    2    50     better
 9. SM101              29  120   140
10. 13

Other links: 

 * FDA

ATCC_13124

Location: /fs/szasmg2/Bacteria/C_perfringens/ATCC_13124/

AA contigs: 

 Name           Length %GC
 1              3256683 28.38

Reads: 

 WGA        51622
 FINISHING   2521
 Total      54143
 * No reads align to SM101 plasmids

SM101

Location: /fs/szasmg2/Bacteria/C_perfringens/SM101

AA contigs: 

 Name           Length %GC
 1              12397  26.68
 2              12206  25.82
 3              2897393 28.25

Reads: 

 WGA        40816
 FINISHING   2994
 Total      543810

Insignia uploads

Assemblies selected: 

   /fs/szasmg2/Bacteria/C_perfringens/ATCC_13124/best -> AA/CS--AI-1565/
   /fs/szasmg2/Bacteria/C_perfringens/B_str__ATCC_3626/best ->    AA/CS--AI-2899/
   /fs/szasmg2/Bacteria/C_perfringens/CPE_str__F4969/best -> 2007_1005_WGA/
   /fs/szasmg2/Bacteria/C_perfringens/C_str__JGS1495/best ->    AA/CS--AI-2889/
   /fs/szasmg2/Bacteria/C_perfringens/E_str__JGS1987/best -> 2007_1005_WGA
   /fs/szasmg2/Bacteria/C_perfringens/SM101/best -> AA/CS--AI-1688/
   /fs/szasmg2/Bacteria/C_perfringens/str__nctc8239/best -> 2007_1005_WGA/
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