Ecoli germany: Difference between revisions
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= Close relatives = | = Close relatives = | ||
NC_011748 | NC_011748 Escherichia coli 55989, complete genome; Length: 5,154,862 nt | ||
NC_011752 Escherichia coli 55989 plasmid 55989p, complete sequence; Length: 72,482 nt | |||
NC_011752 | |||
NC_013353 Escherichia coli O103:H2 str. 12009, complete genome; Length: 5,449,314 nt | |||
NC_013354 Escherichia coli O103:H2 str. 12009 plasmid pO103, complete sequence; Length: 75,546 nt | |||
= Data = | = Data = | ||
* http://www.genomics.cn/en/news_show.php?type=show&id=644 | |||
* ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482/ | |||
= Links = | = Links = | ||
| Line 48: | Line 27: | ||
read alignment: CLC; 85% of untrimmed reads aligned | read alignment: CLC; 85% of untrimmed reads aligned | ||
6X+ cvg regions: 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. | De novo assembly => 3,297 contigs with an N25 of 4K and N50 of 2.5K. | ||
== | == Assembly stats == | ||
. | . elem min q1 q2 q3 max mean n50 sum | ||
ctg+deg | CA.ctg+deg 22395 64 107 159 253 2367 204 216 4567575 | ||
newbler.Ecoli_55989.ctg 8357 100 218 397 696 5038 534 639 4465330 | |||
AMOScmp.Ecoli_55989.ctg 1321 65 425 1780 5257 40345 3774 7775 4985978 | |||
Revision as of 13:36, 5 June 2011
Close relatives
NC_011748 Escherichia coli 55989, complete genome; Length: 5,154,862 nt NC_011752 Escherichia coli 55989 plasmid 55989p, complete sequence; Length: 72,482 nt
NC_013353 Escherichia coli O103:H2 str. 12009, complete genome; Length: 5,449,314 nt NC_013354 Escherichia coli O103:H2 str. 12009 plasmid pO103, complete sequence; Length: 75,546 nt
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
. elem min q1 q2 q3 max mean n50 sum run 629368 5 99 106 109 135 102 107 63944436 run.trimmed 617257 10 46 69 86 94 64 79 39745910
read alignment: CLC; 85% of untrimmed reads aligned 6X+ cvg regions: 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.
Assembly stats
. elem min q1 q2 q3 max mean n50 sum CA.ctg+deg 22395 64 107 159 253 2367 204 216 4567575 newbler.Ecoli_55989.ctg 8357 100 218 397 696 5038 534 639 4465330 AMOScmp.Ecoli_55989.ctg 1321 65 425 1780 5257 40345 3774 7775 4985978