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Search results for pathogen
pathogen
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39 search results found
2019 Wuhan Coronavirus Data
⭐
624
2019 Wuhan Coronavirus data (COVID-19 / 2019-nCoV)
Roary
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219
Rapid large-scale prokaryote pan genome analysis
Amr
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203
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
Circlator
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193
A tool to circularize genome assemblies
Artemis
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191
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
Snp Sites
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173
Finds SNP sites from a multi-FASTA alignment file
Gubbins
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154
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Ariba
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135
Antimicrobial Resistance Identification By Assembly
Assembly Stats
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92
Get assembly statistics from FASTA and FASTQ files
Taxprofiler
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78
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Ancientmetagenomedir
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61
Repository containing lists of all published ancient metagenomic (and related) samples and libraries
Microbetrace
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53
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
Fastaq
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45
Python3 scripts to manipulate FASTA and FASTQ files
Assembly_improvement
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39
Improve the quality of a denovo assembly by scaffolding and gap filling
Pathogen Informatics Training
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38
Iva
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37
de novo virus assembler of Illumina paired reads
Mandrake
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34
Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
Pathogentrack
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22
A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.
Gff3toembl
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20
Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
Tiptoft
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20
Predict plasmids from uncorrected long read data
Phat
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17
Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform
Plasmidtron
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16
Assembling the cause of phenotypes and genotypes from NGS data
Bio Tradis
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15
A set of tools to analyse the output from TraDIS analyses
Darkest Space
⭐
15
Minimal colorscheme for vim.
Seroba
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14
k-mer based Pipeline to identify the Serotype from Illumina NGS reads
Saffrontree
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14
SaffronTree: Reference free rapid phylogenetic tree construction from raw read data
Mlst_check
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14
Multilocus sequence typing by blast using the schemes from PubMLST
Lodestone
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11
Mycobacterial pipeline
Isb_course_2023
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10
Materials and presentation for the 2023 ISB Microbiome course.
Rpops
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8
PoPS (Pest or Pathogen Spread) R Package
Dynamaedes
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7
Model to simulate the population dynamics of four Aedes mosquito species.
Esviritu
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7
Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
Albatradis
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7
Comparative TraDIS analysis
Grdi_amr_one_health
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6
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.
Dotfiles
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5
My dotfiles Installation with Interactive Menu
Minimalsetofviralpeptidome Uniqmin
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5
An alignment-independent tool for the study of pathogen sequence diversity
Pops Core
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5
PoPS Core: C++ library for the Pest or Pathogen Spread Model
Microbetrace
⭐
5
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
Vim Slime Syntax
⭐
5
1-39 of 39 search results
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