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author rakesh4osdd
date Wed, 30 Jun 2021 05:35:56 +0000
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1 # clsi_profile 1 # clsi_profile
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3 CLSI profile for ASIST using the CLSI standards 2020 by AST profiling for bacteria. It help to generate the input file for ASIST program based on MIC values provided by CLSI based AST profiling. 3 CLSI profile for ASIST using the CLSI standards 2020 by AST profiling for bacteria. It help to generate the input file for ASIST program based on MIC values provided by CLSI based AST profiling.
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5 # ASIST: Antimicrobial Susceptibility standards** 5 # ASIST: Antimicrobial Susceptibility standards
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7 In the first column strain names will be mentioned, the second column will be left blank for getting resistance phenotype, starting two rows will comprise antibiotic names (first row) and antibiotic classes (second row). The data for the resistance profile will then start from the C3 column of an excel file which can be converted into a .csv file. Since B3 is left blank, after implementing the algorithm, column B3 will be filled with the resistance phenotype (susceptible, MDR, XDR, PDR). 7 In the first column strain names will be mentioned, the second column will be left blank for getting resistance phenotype, starting two rows will comprise antibiotic names (first row) and antibiotic classes (second row). The data for the resistance profile will then start from the C3 column of an excel file which can be converted into a .csv file. Since B3 is left blank, after implementing the algorithm, column B3 will be filled with the resistance phenotype (susceptible, MDR, XDR, PDR).
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9 **Example Input CSV file:** 9 **Example Input CSV file:**
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11 Strain name,Resistance_phenotype,Antibiotic_A1,Antibiotic_A2,Antibiotic_A_N 11 Strain name,Resistance_phenotype,Antibiotic_A1,Antibiotic_A2,Antibiotic_A_N
12 Strain_1,Phenotype_1,Resistant,Resistant,Resistant 12 Strain_1,Phenotype_1,Resistant,Resistant,Resistant
13 Strain_2,Phenotype_2,Resistant,Susceptible,Resistant 13 Strain_2,Phenotype_2,Resistant,Susceptible,Resistant
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15 Link to the code : https://github.com/rakesh4osdd/asist 15 Link to the code : https://github.com/rakesh4osdd/clsi_profile , https://github.com/rakesh4osdd/asist
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18 # ASIST tool suite 18 # ASIST tool suite
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20 These tools can be install from Galaxy toolshed to a Galaxy installation https://galaxyproject.org/admin/get-galaxy/. 20 These tools can be install from Galaxy toolshed to a Galaxy installation https://galaxyproject.org/admin/get-galaxy/.