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Lists (17)
Starred repositories
A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
Add biological annotations to variants in a given VCF file.
VCF2Dis: A new simple and efficient software to calculate p-distance matrix and construct population phylogeny based Variant Call Format
This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.
RCandy: an R package for visualising homologous recombination events in bacterial genomes
Data associated with paper "Prophage-encoded immune evasion factors are critical for Staphylococcus aureus human and animal host infection, switching and adaptation"
Single-microbe RNA sequencing of the human gut microbiome
Robs manual for the computational genomics and bioinformatics class.
完全免费, 自动获取新账号,一键重置新额度, 解决机器码问题, 自动满额度
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
Subspecies level association study.
All scripts used for the analysis of the twilight of the pan-genome, and scripts available for others to apply similar analysis
A toolbox for pangenome analysis and threshold evaluation.
Signature-SNVs a method for selecting signature SNVs from metagenomic data for input into FEAST for source tracking.
a simple way to call SNPs from fastas. Managed by Peter Laurin
GitHub repository for Mah, Lohmueller, and Garud 2023, bioRxiv
Uses cDBG to count unitigs in bacterial populations
This repository contains all code used in Sawhney & Vargas et al. (2023).
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Updated Jul 25, 2023
Data associated with the manuscript "Acquisition, co-option, and duplication of the rtx toxin system and the emergence of virulence in Kingella" by Morreale et al.
A library of Machine Learning tools to predict antibiotic resistance from NGS data
an interactive viewer for populations of bacterial genomes linked by a phylogeny
"Whole genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming" by Zixi…