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23 search results found

Rapid large-scale prokaryote pan genome analysis

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

Circlator ⭐ 193

A tool to circularize genome assemblies

Artemis ⭐ 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 ⭐ 173

Finds SNP sites from a multi-FASTA alignment file

Antimicrobial Resistance Identification By Assembly

Gubbins ⭐ 133

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Assembly Stats ⭐ 92

Get assembly statistics from FASTA and FASTQ files

Taxprofiler ⭐ 78

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Microbetrace ⭐ 53

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

Python3 scripts to manipulate FASTA and FASTQ files

Assembly_improvement ⭐ 39

Improve the quality of a denovo assembly by scaffolding and gap filling

Pathogen Informatics Training ⭐ 38

de novo virus assembler of Illumina paired reads

Pathogentrack ⭐ 22

A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.

Gff3toembl ⭐ 20

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Predict plasmids from uncorrected long read data

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Plasmidtron ⭐ 16

Assembling the cause of phenotypes and genotypes from NGS data

Bio Tradis ⭐ 15

A set of tools to analyse the output from TraDIS analyses

k-mer based Pipeline to identify the Serotype from Illumina NGS reads

Saffrontree ⭐ 14

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Mlst_check ⭐ 14

Multilocus sequence typing by blast using the schemes from PubMLST

Lodestone ⭐ 11

Mycobacterial pipeline

Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data

Albatradis ⭐ 7

Comparative TraDIS analysis

Microbetrace ⭐ 5

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

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