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make_silva_db

General procedure for making QIIME 2 compatible SILVA reference files

mamba

The Fast Cross-Platform Package Manager

markdown-here

Google Chrome, Firefox, and Thunderbird extension that lets you write email in Markdown and render it before sending.

marker_gene_db.md

bash or python based pipeline for commonly used marker gene db

marmicstats

marvel

MARVEL: Metagenomic Analyses and Retrieval of Viral ELements

masame

Code to run the shiny functions for the MASAME suite

masurca

matrixstats

R package: Methods that Apply to Rows and Columns of Matrices (and to Vectors)

mdm

Workflow and package for network approach to study the role of microbial dark matter (MDM)

megahit

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

megamerge

MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs)

metabolic

A scalable high-throughput metabolic and biogeochemical functional trait profiler

metabolic-hmms

HMM databases for microbial metabolic genes of environmental/biogeochemical importance.

metachip

Horizontal gene transfer (HGT) identification pipeline

metacluster

R package for context-specific functionality analysis of metabolic gene clusters

metaerg

metagem

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

metagenome

metagenome-1

Metagenome analysis pipeline

metagenome_pfam_score

Protocol for finding informative protein families and then using them to score metagenomic sets.

metagenomics-workshop

metagenomics-workshop-1

Metagenomics Workshop

metaphlan

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

metapop

A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations

metasanity

Pipeline for major biological analyses.

metascan

Metabolic scanning and annotation of Metagenomes

metatranscriptomics

Scripts used for the calculation of quantitative transcript metrics TPM and RPKM

metawrap

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

methanoliparum_ms_code