genomewalker

bam-filter

A simple tool to calculate metrics from a BAM file and filter references with uneven coverages

aMGSIM

aMGSIM is an extension of MGSIM to create simulated ancient metagenome reads in multiple microbial synthetic communities.

derep-genomes

A simple genome de-replication tool using fastANI and a bit of graph-based analysis

ebame7

x-filter

A simple tool to filter BLASTx results with special emphasis on ancient DNA studies

collapse-gtdb-tree

A simple tool to collapse a GTDB to a certain rank.

get-biomes

A simple tool to get biomes related data from MGnify and ENA

SpiecEasi

Sparse InversE Covariance estimation for Ecological Association and Statistical Inference

aeGenomicsCourse

aMGSIM-smk

A snakemake workflow to generate multiple synthetic datasets using aMGSIM

ancient-environmental-genomics-course

anvio.org

The anvi'o community web page

bioconda-recipes

Conda recipes for the bioconda channel.

carpedeam-manuscript

decOM

🗑️🦷 decOM 🦷🗑️

dmg-reads

A simple tool to extract damaged reads from BAM files

dotfiles

ebame8

FunDatA

A repository for the Fundamentals Data Analysis course

get-ancient-vf

A simple tool to find virulence factors in ancient metagenomes

get-read-percid

A simple tool to extract references from BAM files and get read statistics

get-reads-taxonomy

A simple tool to extract reads from specific taxonomic groups BAM files

kegg-db-setup

A simple workflow that creates a dereplicated KEGG GENES database by KO.

map-by-node_workflow

metaDMG-core

metaDMG

metaDMG-cpp

metaDMG-cpp

metaDMG-live-dashboard-EBAME7

metaDMG Live Dashboard for EBAME7

MIxS-MInAS.github.io

Website for the MixS-MInAS ancient DNA sequence metadata checklist project

publist

track-duplicates