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assembly-stats

Assembly statistic visualisation

assembly-stats-1

Get assembly statistics from FASTA and FASTQ files

bbmap

(Not Offical) BBMap short read aligner, and other bioinformatic tools.

centrifuge

Classifier for metagenomic sequences

cog

Scripts and steps for making a consolidated COG database file for tools like DIAMOND.

complete-python-3-bootcamp

Course Files for Complete Python 3 Bootcamp Course on Udemy

coverm

Read coverage calculator for metagenomics

data-science-for-life-science

CRT outreach program to assist life scientists in learning basic data science skills.

environmental_metagenomics

A quick workflow to get researchers started with the bioinformatic pipeline used in the Environmental Metagenomics program.

genome_annotation

The genome annotation service provides automated gene annotation based on the RAST system. This deploys both client and service components.

itolapi

Python API for the Interactive Tree of Life (iTOL)

kegg_http_tools

Query KEGG for pathways from KEGG Orthologs (KOs).

magpy

Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)

mangrove-metagenomics

metabolic

A scalable high-throughput metabolic and biogeochemical functional trait profiler

metabolic-hmms

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

metabolishmm

Tool for constructing phylogenies and summarizing metabolic characteristics based on curated and custom profile HMMs

metatranscriptome-workshop

Metatranscriptomics Tutorial

metatranscriptomics-scripts

This repo contains modified python scripts from https://github.com/ParkinsonLab/Metatranscriptome-Workshop

microbialgenomemetagenomecourse

Bioinformatic course on bacterial genomics and metagenomics Helsinki December 2017

microbiome_helper

A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.

nanopore-scripts

Various scripts and recipes for working with nanopore data

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

omixer-rpm

A Reference Pathways Mapper for turning metagenomic functional profiles into pathway/module profiles.

parkinson_int_meta_pipe

meta transcript/genomics pipeline for parkinson lab

pgap

NCBI Prokaryotic Genome Annotation Pipeline

phylogenomics-tools

Scripts for automating tasks in phylogenetics with microbial genomes

phylogenomicsworkflow

A workflow to generate a phylogentic tree with your Genomes

picrust2

Code, unit tests, and tutorials for running PICRUSt2

picrust_database_update

This repo contains updated precalculated files to be used with PICRUSt for prediction of metagenomes from 16S rRNA amplicon sequencing data.