MGnify (@EBI-Metagenomics)
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EBI-Metagenomics

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Top repositories

1

emg-viral-pipeline

VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
Python
116
star
2

genomes-catalogue-pipeline

MGnify genome analysis pipeline
Python
89
star
3

EukCC

Tool to estimate genome quality of microbial eukaryotes
Python
29
star
4

emg-toolkit

MGnify API toolkit
Python
21
star
5

ebi-metagenomics-cwl

This repository contains the CWL description of the EBI Metagenomics pipeline
Common Workflow Language
21
star
6

pipeline-v5

This repository contains all CWL descriptions of the MGnify pipeline version 5.0.
HTML
21
star
7

genome_uploader

Python script to upload bins and MAGs to ENA (European Nucleotide Archive)
Python
20
star
8

MGnifyR

R package for searching, downloading and analysis of EBI MGnify metagenomics data
R
19
star
9

mobilome-annotation-pipeline

Python
16
star
10

notebooks

MGnify documentation and Jupyter Lab notebooks to support downstream analysis of MGnify data (EMBL-EBI's metagenomics platform)
Jupyter Notebook
13
star
11

examples

Microbiome Informatics - API and service usage examples
Jupyter Notebook
12
star
12

ebi-metagenomics

Automatically exported from code.google.com/p/ebi-metagenomics
Java
11
star
13

emgapi

MGnify RESTful API
Python
10
star
14

kegg-pathways-completeness-tool

Python
6
star
15

workflow-is-cwl

This repository contains CWL descriptions of the various tools which will allow you to build workflows for the annotation of transcripts
HTML
6
star
16

mgnify-web

Parent repo for MGnify's (EMBL-EBI's metagenomics platform) API and web client. Designed for local development.
Python
5
star
17

orchestra

A job orchestration system to rule them all
Python
4
star
18

ebi-metagenomics-client

This repos contains the MGnify web client
TypeScript
4
star
19

amplicon-pipeline

Nextflow
4
star
20

motus_pipeline

Raw reads mOTUs and taxonomic classification pipeline
HTML
3
star
21

CWL-assembly

Common Workflow Language
3
star
22

MGnifam

Python
3
star
23

fasta-reader-py

FASTA file reader.
Python
3
star
24

EMG-docs

This repository contains the documentation for the EBI Metagenomics resource
3
star
25

holofood-course

ReadTheDocs/Sphinx documentation source for the "Organisation and utilisation of hologenomic datasets" Holofood course, 2022
HTML
3
star
26

nf-modules

Microbiome Informatics NF modules and sufworkflows
Nextflow
3
star
27

mgnify-biata-2020

2
star
28

CRISPRCasFinder-CWL

Implementation of CRIPSPRCasFinder tool in CWL
Common Workflow Language
2
star
29

fetch_tool

Tool which allows you to fetch RAW read files from the European Nucleotide Archive (ENA)
Python
2
star
30

mgnify-sourmash-component

A web component that let you select FastA or FastQ sequence files and creates sketches (KmerMinHash signatures) using Sourmash.
TypeScript
2
star
31

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
HTML
2
star
32

hmmer-py-old

HMMER Python interface.
Python
2
star
33

mgnify-ebi-2020

1
star
34

hmmer-reader-py

HMMER file reader.
Python
1
star
35

fraggenescan

FragGene Scan fork
C
1
star
36

genome-search

Microservice API for searching fragments against indexed genomes, using COBS. Provides the "search by gene" feature on MGnify's MAG catalogues.
Python
1
star
37

mgnify-ebi-2021

Jupyter Notebook
1
star
38

green-socket

Abstraction for non-blocking sockets in C.
C
1
star
39

hmmer3

HMMER (version 3) related projects
C
1
star
40

fasta-reader

FASTA reader for C.
C
1
star
41

ebi-metagenomics-stats

Python
1
star
42

HoloFoodR

R interface for HoloFood resource
R
1
star
43

mgnifams-site

JavaScript
1
star
44

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.
Python
1
star
45

ena-api-handler

Python
1
star
46

biome_prediction

Python module to predict GOLD biomes from free text field, can also be used as a command line tool.
Python
1
star
47

mgbinrefinder

Bin refinment tool
Python
1
star
48

mgnifams

Python
1
star