Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
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Updated
Jun 12, 2024 - Python
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
sensitive and precise assembly of short sequencing reads
AMR/VF LGT focused bacterial genomics analysis workflow
A collection of Galaxy-related training material
🦠📇 Genomes to report pipeline - for Bacteria and Archaea
Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes
🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
🦠🧬 Unraveling Viral Genomes from Metagenomes
Application for analysis of targeted metagenomics sequencing data. Intended for use with multiplexed Illumina short-read data generated after enrichment.
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.
An analysis and visualization platform for 'omics data
A flexible metagenomic pipeline combining read-based, assemblies and MAGs with downstream analysis
MMseqs2: ultra fast and sensitive search and clustering suite
MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
Data processing scripts for analysis of targeted metagenomics sequencing data. Intended for use with multiplexed Illumina short-read data generated after enrichment.
TrIdent- Transduction Identification: Automatic detection, classification and characterization of active transduction events in microbiomes.
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.
Reconstruction and analysis of viral and host genomes at multi-organ level
CAMISIM: Simulating metagenomes and microbial communities
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