pathogen
Here are 90 public repositories matching this topic...
Data processing scripts for analysis of targeted metagenomics sequencing data. Intended for use with multiplexed Illumina short-read data generated after enrichment.
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Jun 11, 2024 - Python
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
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Jun 11, 2024 - Nextflow
Nextstrain build for novel coronavirus SARS-CoV-2
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Jun 7, 2024 - Python
Scripts. config, and snakefiles for seasonal-flu nextstrain builds
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Jun 7, 2024 - Python
SARS-CoV-2 variant growth rates and frequency forecasts
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Jun 7, 2024 - Python
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
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Jun 7, 2024 - Python
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
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Jun 6, 2024 - C++
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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Jun 11, 2024 - Python
Nextstrain build for mpox virus
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Jun 11, 2024 - Python
An open-source project to create a centralized hub for live streaming content.
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Jun 5, 2024 - HTML
Code repository for the publication: "Genomic evidence of contemporary hybridization between Schistosoma species"
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Jun 4, 2024 - Python
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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May 31, 2024
StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.
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May 31, 2024 - C++
This repository contains all changes made to the strain specific models of Corynebacterium striatum.
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May 22, 2024 - HTML
Pathogen Informatics Center: Analysis, Networking, Translation & Education
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May 21, 2024 - Shell
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