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2018-11-30-nuig

Sample Website for Instructor Training

amphora2

An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.

anadama2

AnADAMA2 is the next generation of AnADAMA (Another Automated Data Analysis Management Application). AnADAMA is a tool to capture your workflow and execute it efficiently on your local machine or in a grid compute environment (ie. sun grid engine or slurm).

annofilt

Filter Prokka assemblies for pangenome analysis

benchmarkmicrobiome

Large-scale Benchmarking of Microbial Multivariable Association Methods

blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

boxr

:package: A high-level R interface for the box.com API

bugbuilder

Hands-free microbial genome assembly

cafe

:flags: :ocean: CAFE is a genomic island Prediction tool

cgfind

Minimal way to find and download complete prokaryotic genomes

cheapwine

checkm

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes

chordomics

comparison_of_da_microbiome_methods

corncob

Count Regression for Correlated Observations with the Beta-binomial

curveball

Predicting microbial growth in a mixed culture from growth curve data

dada2

Accurate sample inference from amplicon data with single nucleotide resolution

etoki

all methods related to Enterobase

ezclermont

Phylotype your strains using Clermont's 2013 method: ezclermont.org

fcid

gemini

:gem: Genome mining tool-- Identifies regions of atypicality

genvis_lite

getupandrunning

Dear Future Me; this is to help get your system back to normal after Current You does something foolish.

happie

Horizontally Aquired Partial Pangenome of Inserted Elements

hecatomb

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data

hh_plate

NUIG Hacky Hour Plate Reader Example

humann

HUMAnN 3.0 is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

isabl_cli

🤖 isabl Command Line Client and SDK.

isescan

A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome

isfinder_database

download isfinder database