Pinned Repositories
aMGSIM
aMGSIM is an extension of MGSIM to create simulated ancient metagenome reads in multiple microbial synthetic communities.
bam-filter
A simple tool to calculate metrics from a BAM file and filter references with uneven coverages
collapse-gtdb-tree
A simple tool to collapse a GTDB to a certain rank.
derep-genomes
A simple genome de-replication tool using fastANI and a bit of graph-based analysis
EBAME4
ebame7
microbeco2015
p2p
refine-contigs
A simple tool to identify and clean misassemblies for ancient metagenomics
x-filter
A simple tool to filter BLASTx results with special emphasis on ancient DNA studies
genomewalker's Repositories
genomewalker/bam-filter
A simple tool to calculate metrics from a BAM file and filter references with uneven coverages
genomewalker/aMGSIM
aMGSIM is an extension of MGSIM to create simulated ancient metagenome reads in multiple microbial synthetic communities.
genomewalker/derep-genomes
A simple genome de-replication tool using fastANI and a bit of graph-based analysis
genomewalker/ebame7
genomewalker/x-filter
A simple tool to filter BLASTx results with special emphasis on ancient DNA studies
genomewalker/collapse-gtdb-tree
A simple tool to collapse a GTDB to a certain rank.
genomewalker/get-biomes
A simple tool to get biomes related data from MGnify and ENA
genomewalker/SpiecEasi
Sparse InversE Covariance estimation for Ecological Association and Statistical Inference
genomewalker/aeGenomicsCourse
genomewalker/aMGSIM-smk
A snakemake workflow to generate multiple synthetic datasets using aMGSIM
genomewalker/ancient-environmental-genomics-course
genomewalker/anvio.org
The anvi'o community web page
genomewalker/bioconda-recipes
Conda recipes for the bioconda channel.
genomewalker/carpedeam-manuscript
genomewalker/decOM
🗑️🦷 decOM 🦷🗑️
genomewalker/dmg-reads
A simple tool to extract damaged reads from BAM files
genomewalker/dotfiles
genomewalker/ebame8
genomewalker/FunDatA
A repository for the Fundamentals Data Analysis course
genomewalker/get-ancient-vf
A simple tool to find virulence factors in ancient metagenomes
genomewalker/get-read-percid
A simple tool to extract references from BAM files and get read statistics
genomewalker/get-reads-taxonomy
A simple tool to extract reads from specific taxonomic groups BAM files
genomewalker/kegg-db-setup
A simple workflow that creates a dereplicated KEGG GENES database by KO.
genomewalker/map-by-node_workflow
genomewalker/metaDMG-core
metaDMG
genomewalker/metaDMG-cpp
metaDMG-cpp
genomewalker/metaDMG-live-dashboard-EBAME7
metaDMG Live Dashboard for EBAME7
genomewalker/MIxS-MInAS.github.io
Website for the MixS-MInAS ancient DNA sequence metadata checklist project
genomewalker/publist
genomewalker/track-duplicates