Ecoli germany: Difference between revisions
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= Close relatives = | |||
NC_011748 | NC_011748 | ||
Escherichia coli 55989, complete genome | Escherichia coli 55989, complete genome | ||
| Line 26: | Line 26: | ||
Created: 2009/10/07 | Created: 2009/10/07 | ||
= Data = | |||
http://www.genomics.cn/en/news_show.php?type=show&id=644 | http://www.genomics.cn/en/news_show.php?type=show&id=644 | ||
ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482/ | ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482/ | ||
= Links = | |||
* http://www.iontorrent.com/ | * http://www.iontorrent.com/ | ||
* http://omicsomics.blogspot.com/2011/05/ion-torrents-data-quality-is-pretty.html | * http://omicsomics.blogspot.com/2011/05/ion-torrents-data-quality-is-pretty.html | ||
* http://pathogenomics.bham.ac.uk/blog/2011/05/first-look-at-ion-torrent-data-de-novo-assembly/ | * http://pathogenomics.bham.ac.uk/blog/2011/05/first-look-at-ion-torrent-data-de-novo-assembly/ | ||
= Assemblies = | |||
== EdgeBio CLC & newbler == | |||
* http://www.edgebio.com/data/ion/ecoli_bgi/ | * http://www.edgebio.com/data/ion/ecoli_bgi/ | ||
read QC: FastQC | read QC: FastQC | ||
| Line 45: | Line 49: | ||
De novo assembly => 3,297 contigs with an N25 of 4K and N50 of 2.5K. | De novo assembly => 3,297 contigs with an N25 of 4K and N50 of 2.5K. | ||
== CA == | |||
. elem min q1 q2 q3 max mean n50 sum | |||
ctg+deg 22395 64 107 159 253 2367 204 216 4567575 | |||
== newbler.refMapper Ecoli_55989 == | |||
. elem min q1 q2 q3 max mean n50 sum | |||
ctg 8357 100 218 397 696 5038 534 639 4465330 | |||
Revision as of 15:02, 3 June 2011
Close relatives
NC_011748 Escherichia coli 55989, complete genome DNA; circular; Length: 5,154,862 nt Replicon Type: chromosome Created: 2008/12/16 NC_011752 Escherichia coli 55989 plasmid 55989p, complete sequence DNA; circular; Length: 72,482 nt Replicon Type: plasmid Replicon Name: 55989p Created: 2008/12/161
NC_013353 Escherichia coli O103:H2 str. 12009, complete genome DNA; circular; Length: 5,449,314 nt Replicon Type: chromosome Created: 2009/10/08 NC_013354 Escherichia coli O103:H2 str. 12009 plasmid pO103, complete sequence DNA; circular; Length: 75,546 nt Replicon Type: plasmid Replicon Name: pO103 Created: 2009/10/07
Data
http://www.genomics.cn/en/news_show.php?type=show&id=644 ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482/
Links
- http://www.iontorrent.com/
- http://omicsomics.blogspot.com/2011/05/ion-torrents-data-quality-is-pretty.html
- http://pathogenomics.bham.ac.uk/blog/2011/05/first-look-at-ion-torrent-data-de-novo-assembly/
Assemblies
EdgeBio CLC & newbler
read QC: FastQC read trimming: CLC read alignment: CLC; 85% of untrimmed reads aligned 6X+ cvg redgions: 490 SNPS s & 1,848 INDELS.
De novo assembly of 90K reads that did not map, 58K assembled together => 363 contigs ranging in size from 400 to 7800 bp. Contigs were blasted against NRNT at NCBI with a minimum .01 e-value. Hits: E. coli strains (such as O83:H1 and O42) , Shigella flexneri, Salmonella, and Cronobacter.
De novo assembly => 3,297 contigs with an N25 of 4K and N50 of 2.5K.
CA
. elem min q1 q2 q3 max mean n50 sum ctg+deg 22395 64 107 159 253 2367 204 216 4567575
newbler.refMapper Ecoli_55989
. elem min q1 q2 q3 max mean n50 sum ctg 8357 100 218 397 696 5038 534 639 4465330