Ecoli germany: Difference between revisions
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ctg 1217 100 251 938 5215 72019 4274 13577 5201850 | ctg 1217 100 251 938 5215 72019 4274 13577 5201850 | ||
ctg.v2 513 62 346 896 4903 204342 10330 53266 5299150 | ctg.v2 513 62 346 896 4903 204342 10330 53266 5299150 | ||
* [http://www.ncbi.nlm.nih.gov/nuccore/AFOG00000000 Escherichia coli TY-2482, whole genome shotgun sequencing project @NCBI] | |||
= Links = | = Links = | ||
Revision as of 14:07, 7 June 2011
Finished genomes
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
- BGI Sequences Genome of the Deadly E. Coli in Germany and Reveals New Super-Toxic Strain June 2nd 2011
- BGI run1-7 & assembly
. elem min q1 q2 q3 max mean n50 sum run1 92370 5 99 106 109 123 102 107 9433083 run2 122208 5 96 105 109 133 100 106 12248530 run3 96765 5 100 106 110 129 103 107 9958873 run4 222275 5 101 107 110 135 103 107 22924825 run5 95750 5 92 103 108 133 97 104 9379125 run1-5 629368 5 99 106 109 135 102 107 63944436 (12.2X) run6 79341 5 104 108 111 137 105 108 8355410 run7 74388 5 97 105 109 129 100 106 7469876 run1-7 783097 5 99 106 110 137 102 107 79769722 (15.2X) ctg 1217 100 251 938 5215 72019 4274 13577 5201850 ctg.v2 513 62 346 896 4903 204342 10330 53266 5299150
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/
- [1]
EdgeBio Assembly
- Used CLC & newbler
- http://www.edgebio.com/data/ion/ecoli_bgi/
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.
CBCB best assembly
- run1-5
. elem min q1 q2 q3 max mean n50 sum ctg 505 35 204 758 8927 185186 9823 41503 4960767 ctg.denovo 4261 31 41 58 104 2713 119 31 506842 total 4766 31 44 59 161 185186 1147 41503 5467609
- run1-7
. elem min q1 q2 q3 max mean n50 sum ctg 445 41 202 651 7622 185186 11156 46725 4964630 ctg.denovo 4704 31 39 57 88 2990 113 31 531947 total 5149 31 40 58 129 185186 1068 46725 5496577
- Method (run1-5):
The reads were first assembled using Ecoli_55989 as reference. The unmapped reads were assembled denovo using ABYSS. total reads: 629,368 reads aligned to Ecoli_55989 using "bwa bwasw": 545,233 (the consensus was called using "samtools pileup") unaligned reads : 84,135
- Ftp file locations (run1-5)
ftp://ftp.cbcb.umd.edu/pub/data/assembly/Ecoli_TY-2482/ ftp://ftp.cbcb.umd.edu/pub/data/assembly/Ecoli_TY-2482/assemble.sh ftp://ftp.cbcb.umd.edu/pub/data/assembly/Ecoli_TY-2482/asm.summary ftp://ftp.cbcb.umd.edu/pub/data/assembly/Ecoli_TY-2482/asm.ctg.fasta ftp://ftp.cbcb.umd.edu/pub/data/assembly/Ecoli_TY-2482/asm.ctg.denovo.fasta
Other CBCB assemblies run1-5
. 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