EBI-Metagenomics/EukCC

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Created almost 5 years ago
Updated 10 months ago

EBI-Metagenomics/EukCC

EBI-Metagenomics

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Tool to estimate genome quality of microbial eukaryotes

emg-viral-pipeline

VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies

genomes-catalogue-pipeline

MGnify genome analysis pipeline

emg-toolkit

MGnify API toolkit

ebi-metagenomics-cwl

This repository contains the CWL description of the EBI Metagenomics pipeline

Common Workflow Language

pipeline-v5

This repository contains all CWL descriptions of the MGnify pipeline version 5.0.

genome_uploader

Python script to upload bins and MAGs to ENA (European Nucleotide Archive)

MGnifyR

R package for searching, downloading and analysis of EBI MGnify metagenomics data

mobilome-annotation-pipeline

notebooks

MGnify documentation and Jupyter Lab notebooks to support downstream analysis of MGnify data (EMBL-EBI's metagenomics platform)

Jupyter Notebook

examples

Microbiome Informatics - API and service usage examples

Jupyter Notebook

ebi-metagenomics

Automatically exported from code.google.com/p/ebi-metagenomics

emgapi

MGnify RESTful API

kegg-pathways-completeness-tool

workflow-is-cwl

This repository contains CWL descriptions of the various tools which will allow you to build workflows for the annotation of transcripts

mgnify-web

Parent repo for MGnify's (EMBL-EBI's metagenomics platform) API and web client. Designed for local development.

orchestra

A job orchestration system to rule them all

ebi-metagenomics-client

This repos contains the MGnify web client

amplicon-pipeline

motus_pipeline

Raw reads mOTUs and taxonomic classification pipeline

CWL-assembly

Common Workflow Language

MGnifam

fasta-reader-py

FASTA file reader.

EMG-docs

This repository contains the documentation for the EBI Metagenomics resource

holofood-course

ReadTheDocs/Sphinx documentation source for the "Organisation and utilisation of hologenomic datasets" Holofood course, 2022

nf-modules

Microbiome Informatics NF modules and sufworkflows

mgnify-biata-2020

CRISPRCasFinder-CWL

Implementation of CRIPSPRCasFinder tool in CWL

Common Workflow Language

fetch_tool

Tool which allows you to fetch RAW read files from the European Nucleotide Archive (ENA)

mgnify-sourmash-component

A web component that let you select FastA or FastQ sequence files and creates sketches (KmerMinHash signatures) using Sourmash.

ebi-metagenomics-webkit

NPM package for a Backbone-JS API to consume the European Bioinformatic Institute's MGnify API for metagenomic data, in addition to a widget library to visualise the data

hmmer-py-old

HMMER Python interface.

mgnify-ebi-2020

hmmer-reader-py

HMMER file reader.

fraggenescan

FragGene Scan fork

genome-search

Microservice API for searching fragments against indexed genomes, using COBS. Provides the "search by gene" feature on MGnify's MAG catalogues.

mgnify-ebi-2021

Jupyter Notebook

green-socket

Abstraction for non-blocking sockets in C.

hmmer3

HMMER (version 3) related projects

fasta-reader

FASTA reader for C.

ebi-metagenomics-stats

HoloFoodR

R interface for HoloFood resource

mgnifams-site

holofood-database

HoloFood is a project investigating sustainable food production through hologenomics. This Django app is the data portal where samples and other datasets from the project are made publicly available.

ena-api-handler

biome_prediction

Python module to predict GOLD biomes from free text field, can also be used as a command line tool.

mgbinrefinder

Bin refinment tool

mgnifams