pathogen
Here are 94 public repositories matching this topic...
Scripts. config, and snakefiles for seasonal-flu nextstrain builds
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Jul 29, 2024 - Python
A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.
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Jul 29, 2024 - Python
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Jul 29, 2024 - Python
Nextstrain build for novel coronavirus SARS-CoV-2
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Jul 27, 2024 - Python
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Jul 25, 2024 - Python
Mycobacterial pipeline
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Jul 24, 2024 - Python
SARS-CoV-2 variant growth rates and frequency forecasts
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Jul 18, 2024 - Python
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
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Jul 26, 2024 - Nextflow
A data specification for harmonizing One Health AMR pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a spreadsheet collection template, supported by field and reference guides as well as different curation and new term request SOPs.
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Jul 18, 2024
A data specification for harmonizing One Health Canadian COVID pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a the DataHarmonizer, supported by field and reference guides as well as different curation and new term request SOPs.
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Jul 17, 2024
Repository containing lists of all published ancient metagenomic (and related) samples and libraries
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Jul 24, 2024 - HTML
Nextstrain build for mpox virus
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Jul 25, 2024 - Python
metagenomics pipeline supporting The UnO Project for identifying pathogens in common across outbreak samples
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Jul 29, 2024 - Nextflow
StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.
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Jul 29, 2024 - C++
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