Ecoli germany: Difference between revisions
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* Close relatives ? | * Close relatives ? | ||
NC_011748 | NC_011748 | ||
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Replicon Name: pO103 | Replicon Name: pO103 | ||
Created: 2009/10/07 | 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/ | |||
* 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/ | |||
* http://www.edgebio.com/data/ion/ecoli_bgi/ | |||
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. | |||
Revision as of 14:19, 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/
- 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/
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.