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T1  - Bacterial Genomic Epidemiology with Mixed Samples 
SN  -  /  
UR  - http://hdl.handle.net/10138/336390 
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A1  - Mäklin, Tommi; Kallonen, Teemu; Alanko, Jarno; Samuelsen, Ørjan; Hegstad, Kristin; Mäkinen, Veli; Corander, Jukka; Heinz, Eva; Honkela, Antti 
A2  -  
PB  -  
Y1  - 2021 
LA  - eng 
AB  - Genomic epidemiology is a tool for tracing transmission of pathogens based on whole-genome sequencing. We introduce the mGEMS pipeline for genomic epidemiology with plate sweeps representing mixed samples of a target pathogen, opening the possibility to sequence all colonies on selective plates with a single DNA extraction and sequencing step. The pipeline includes the novel mGEMS read binner for probabilistic assignments of sequencing reads, and the scalable pseudoaligner Themisto. We demonstra... 
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KW  - ALGORITHM; CULTURE; DIVERSITY; EMERGENCE; ESCHERICHIA-COLI; METAGENOMICS; POPULATION-STRUCTURE; R PACKAGE; SINGLE-CELL; STRATEGIES; genomic epidemiology; pathogen surveillance; plate sweeps; probabilistic modelling; pseudoalignment; 11832 Microbiology and virology; 1184 Genetics, developmental biology, physiology 
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