Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
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Updated
May 12, 2024 - Shell
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data
A pipeline for viral identification from metagenomic samples
Reconstruction and analysis of viral and host genomes at multi-organ level
DEPRECATED: Use Cenote-Taker 3 instead
Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
Profiler for metagenomics based on NGLess
This pipeline is intended to be a convenient way to work though large sets of metagenomic or metatranscriptiomic datasets while also retaining high analytical flexibility due to retained intermediate results that might be useful outside of the intended purpose.
Genome-centric Multi-omic Analysis Workflow for the Marinimicrobia paper
a sequence analysis workflow for low-input nanopore sequencing
Quantitative metagenomic alignment and taxonomic exact-matching
Simple script to generate Krona charts for all samples in an OTU table file
RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.
MetaFX – library for feature extraction from whole-genome metagenome sequencing data
Metagenomic functional annotation pipeline
Improve your metagenomic reference sequence: Simple adapter and contamination FASTA masking using bowtie2 and bedtools
A collection of NGLess modules open to community contributions
NGS4ECOPROD - An easy-to-use conda environment and pipelines for metagenome sequence analysis
Use one command to perform genome-centric metagenomics using state-of-the-art methods
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