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ohnoseq edited this page Jun 17, 2011 · 25 revisions

Annotations

TY-2482

  1. 2-Jun Era7 annotation Marina Manrique & Raquel Tobes, (2/6/2011). Nick Loman's assembly from the 2/6/2011 was annotated with BG7 system. Results of Era7 annotations Era7 e. coli TY2482 annotation with bg7 system and annotation files here

  2. 2-Jun Simon Gladman and Torsten Seemann also annotated Nick's assembly from the 2/6/2011. They used a in-house annotation method and reordered the contigs with E. coli EAEC 55989 and TWEC. Results after reordering with E. coli EAEC 55989 here and with TWEC here

  3. 6-Jun Mariam Rizkallah has done automatic annotations with RAST

  4. 7-Jun Annotation of the second BGI's assembly (BGI V2) of E. coli TY-2482 genome. BG7 system was used to perform this anotation. BG7 system. Results of Era7 annotations Era7 annotation of BGI V2 assembly of E. coli TY-2482 and annotation files here

  5. 11-Jun Annotation of the third BGI's assembly (BGI V3) of E. coli TY-2482 genome with BG7. Results of Era7 annotations Automatic annotation of BGI V3 assembly of E. coli TY-2482 genome

  6. 14-Jun Preliminary Manual annotation of two plasmid-derived scaffolds, 29 and 124 from Lisa Crossman comments and [EMBL file annotations here] (http://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/tree/master/strains/TY2482/seqProject/BGI/annotations/Crossman_plasmid_scaffolds)

  7. 16-Jun Marina Manrique & Raquel Tobes (Era7) Automatic annotations of BGI latest assembly (Illumina reads, no gaps) of the chromosome and 3 plasmids of the isolate TY-2482. Files in the [repository] (https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/tree/master/strains/TY2482/seqProject/BGI/annotations/era7bioinformatics/era7_BGI_V4_annotation)

LB226692

  1. 6-Jun David Vallenet A preliminary list of 240 genes of interest is available in the MicroScope platform pdf, xls.

  2. 8-Jun Raquel Tobes & Marina Manrique Era7 automatic annotation of E. coli LB226692 genome (Life Tech and University of Muenster assembly) with BG7 system. Results of Era7 LB226692 annotations Era7 E. coli LB226692 annotation with BG7 system. Annotation result files here https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/tree/master/strains/LB226692/annotations/era7bioinformatics

H112180280

  1. 10-Jun Tim Dallman (HPA) Annotation of H112180280 strain. This was performed using reciprocal BLAST annotation pipeline developed by Anthony Underwood (HPA)

  2. 11-Jun Marina Manrique Era7 automatic annotation of E. coli H112180280 genome (Health Protection Agency genome) with BG7. Results of Era7 H112180280 annotations Automatic annotation of E. coli H112180280 strain (HPA sequence and assembly). Annotation result files [here] (https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/tree/master/strains/H112180280/seqProject/HealthProtectionAgencyUK/annotations/era7bioinformatics/era7_HPA_H112180280_annotations)

  3. 16-Jun Marina Manrique & Raquel Tobes (Era7) Automatic annotation of second HPA assembly of H112180280 isolate. Files in the [repository] (https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/tree/master/strains/H112180280/seqProject/HealthProtectionAgencyUK/annotations/era7bioinformatics/era7_HPA_V2_H112180280_annotation)

GOS1

  1. 15-Jun G2L annotation of their own assembly of GOS1 isolate. Annotation files in the [repository] (https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/tree/master/strains/GOS1/seqProject/G2L/annotations/G2L)

  2. 16-Jun Marina Manrique & Raquel Tobes (Era7) Automatic annotation of G2L assembly of GOS1 isolate. Annotation files in the [repository] (https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/tree/master/strains/GOS1/seqProject/G2L/annotations/era7bioinformatics/era7_G2L_EHEC_GOS1_annotations)

GOS2

  1. 15-Jun G2L annotation of their own assembly of GOS2 isolate. Annotation files in the [repository] (https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/tree/master/strains/GOS2/seqProject/G2L/annotations/G2L)

  2. 17-Jun Marina Manrique & Raquel Tobes (Era7) Automatic annotation of G2L assembly of GOS2 isolate. Annotation files in the [repository] (https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/tree/master/strains/GOS2/seqProject/G2L/annotations/era7bioinformatics/Era7_GOS2_annotation)

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