Results

This page contains links to all results from the exercise 1-6.

Exercise 1

KmerFinder

Kleb7    Kleb9    Kleb10    Unknown_draft_genome

MLST

Kleb7    Kleb9    Kleb10    Unknown_draft_genome

ResFinder

Kleb7    Kleb9    Kleb10    Unknown_draft_genome

PlasmidFinder

Kleb7    Kleb9    Kleb10    Unknown_draft_genome

Exercise 2

KmerFinder

MRSA1-group

ERR070039-P11    ERR108054-P15    ERR128707-P26    ERR128718-HW    ERR070041-not-outbreak

MRSA2-group

ERR070040-P12    ERR124435-P24    ERR124434-P22    ERR128716-HW    ERR070035-not-outbreak

Ecoli1-group

ec11-4632_c1    ec11-5538    c236-11    ec11-3677    ec09-7901

Ecoli2-group

ec11-4623    ec11-5537    c227-11    ec11-3798    ec04-8351

MLST

MRSA1-group

ERR070039-P11    ERR108054-P15    ERR128707-P26    ERR128718-HW    ERR070041-not-outbreak

MRSA2-group

ERR070040-P12    ERR124435-P24    ERR124434-P22    ERR128716-HW    ERR070035-not-outbreak

Ecoli1-group

ec11-4632_c1    ec11-5538    c236-11    ec11-3677    ec09-7901

Ecoli2-group

ec11-4623    ec11-5537    c227-11    ec11-3798    ec04-8351

ResFinder

MRSA1-group

ERR070039-P11    ERR108054-P15    ERR128707-P26    ERR128718-HW    ERR070041-not-outbreak

MRSA2-group

ERR070040-P12    ERR124435-P24    ERR124434-P22    ERR128716-HW    ERR070035-not-outbreak

Ecoli1-group

ec11-4632_c1    ec11-5538    c236-11    ec11-3677    ec09-7901

Ecoli2-group

ec11-4623    ec11-5537    c227-11    ec11-3798    ec04-8351

PlasmidFinder

MRSA1-group

ERR070039-P11    ERR108054-P15    ERR128707-P26    ERR128718-HW    ERR070041-not-outbreak

MRSA2-group

ERR070040-P12    ERR124435-P24    ERR124434-P22    ERR128716-HW    ERR070035-not-outbreak

Ecoli1-group

ec11-4632_c1    ec11-5538    c236-11    ec11-3677    ec09-7901

Ecoli2-group

ec11-4623    ec11-5537    c227-11    ec11-3798    ec04-8351

Exercise 3

SerotypeFinder

Ecoli1-group

ec11-4632_c1    ec11-5538    c236-11    ec11-3677    ec09-7901

Ecoli2-group

ec11-4623    ec11-5537    c227-11    ec11-3798    ec04-8351

VirulenceFinder

Ecoli1-group

ec11-4632_c1    ec11-5538    c236-11    ec11-3677    ec09-7901

Ecoli2-group

ec11-4623    ec11-5537    c227-11    ec11-3798    ec04-8351

MyDBFinder

Ec4 (PapG positive)

Ecoli1-group

ec11-4632_c1    ec11-5538    c236-11    ec11-3677    ec09-7901

Ecoli2-group

ec11-4623    ec11-5537    c227-11    ec11-3798    ec04-8351

Exercise 4

NDtree

MRSA1 (ref: HO 5096 0412. P11, P15, P26, HW, not-outbreak)

MRSA1 without the outlier (ref: HO 5096 0412. P11, P15, P26, HW)

MRSA2 (ref: HO 5096 0412. P12, P24, P22, HW, not-outbreak)

MRSA2 without the outlier (ref: HO 5096 0412. P12, P24, P22, HW)

Ecoli1 (ref: 2011C-3493. ec11-4632_c1, ec11-5538, c236-11, ec11-3677, ec09-7901)

Ecoli1 without the outlier (ref: 2011C-3493. ec11-4632_c1, ec11-5538, c236-11, ec11-3677)

Ecoli2 (ref: 2011C-3493. Ec11-4623, ec11-5537, c227-11, ec11-3798, ec04-8351)

Ecoli2 without the bad-quality strain: Ecoli2 (ref: 2011C-3493. Ec11-4623, ec11-5537, c227-11, ec04-8351)

Ecoli2 without the bad-quality strain and the outlier: Ecoli2 (ref: 2011C-3493. Ec11-4623, ec11-5537, c227-11)

CSIPhylogeny

MRSA1 (ref: HO 5096 0412. P11, P15, P26, HW, not-outbreak)

MRSA1 without the outlier (ref: HO 5096 0412. P11, P15, P26, HW)

MRSA2 (ref: HO 5096 0412. P12, P24, P22, HW, not-outbreak)

MRSA2 without the outlier (ref: HO 5096 0412. P12, P24, P22, HW)

Ecoli1 (ref: 2011C-3493. ec11-4632_c1, ec11-5538, c236-11, ec11-3677, ec09-7901)

Ecoli1 without the outlier (ref: 2011C-3493. ec11-4632_c1, ec11-5538, c236-11, ec11-3677)

Ecoli2 (ref: 2011C-3493. Ec11-4623, ec11-5537, c227-11, ec11-3798, ec04-8351)

Ecoli2 without the bad-quality strain: Ecoli2 (ref: 2011C-3493. Ec11-4623, ec11-5537, c227-11, ec04-8351)

Ecoli2 without the bad-quality strain and the outlier: Ecoli2 (ref: 2011C-3493. Ec11-4623, ec11-5537, c227-11)

Exercise 5

You may login to CGE using an account specific for you. To see your username look at the list of participants. The password is 1234.

Exercise 6

MGMapper outbreak_matrix_pathogen.fastq results