This is a pipeline for exploring viruses (ssDNA, dsDNA phage, and giant DNA viruses) and viral diversity in metagenomes.
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Updated
Jun 10, 2024 - Python
This is a pipeline for exploring viruses (ssDNA, dsDNA phage, and giant DNA viruses) and viral diversity in metagenomes.
Lightweight bioinformatics pipeline for microbial genome recovery
Meteor is a plateform for quantitative metagenomics profiling of complex ecosystems. Meteor relies on genes catalogue to perform specie level taxonomic assignments and functional analysis.
Repository for the presentation of work developed by the student Duarte Velho for the UC Project, of the Master in Bioinformatics of the University of Minho, academic year 23-24.
A flexible metagenomic pipeline combining read-based, assemblies and MAGs with downstream analysis
TAXnomic Profile Aggregation and STAndardisation
AMR/VF LGT focused bacterial genomics analysis workflow
TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various use-cases of mNGS in mind.
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.
🦠📇 Genomes to report pipeline - for Bacteria and Archaea
An analysis and visualization platform for 'omics data
🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs
CAMISIM: Simulating metagenomes and microbial communities
Nanomotif - a tool for identifying methylated motifs in metagenomic samples
ATLAS - Three commands to start analyzing your metagenome data
🦠🧬 Unraveling Viral Genomes from Metagenomes
Metagenomics and Metatranscriptomics pipeline
CroCoDeEL is a tool that detects cross-sample contamination in shotgun metagenomic data
Deepurify is a tool to filter the contaminated contigs in a MAG with a language model.
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