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basicfiltering

Basic filtering scripts for various mutation calling tools

blast_getlca

Python script to parse blast files and assign each read to the taxonomic of the lowest common ancestor

flextaxd

FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )

genome-assembly-programming-challenge

Genome Assembly, de Bruijn Graph, Overlap Graph, Bubbles and Tips Removal, Optimal K-mer, Phi X174 Genome, Error-Prone Reads, Universal Circular String, Eulerian Cycle.

getlca

humann

HUMAnN 2.0 is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

metagenomics

metagenomics-1

Collection of python scripts used in the analysis of long and short read metagenomic data. Includes scripts for taxonomic analysis as well functional annotation of WGS and proteomic data

metagenomics_basic

Basic analysis of metagenomics from assembly to gene abundance

metagenomics_summer_school

Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in December

metagenomicstree

Data processing tree for metagenomics

metamap

Snakemake workflow to map and quantify microbial genomes in metagenomic reads

pindel_germlinecaller

CWL project with Pindel germline calling and filtering

prepare-kegg-for-humann2

py-metagenomics

Some python libs and scripts for metagenomic analyses