All Published Workflows
6 workflows that have been reviewed and published
ATLAS - Three commands to start analyzing your metagenome data
Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, t...
raw sequence reads
Genome assembly
Annotation track
checkm2
gunc
prodigal
snakemake-wrapper-utils
MEGAHIT
Atlas
BBMap
Biopython
BioRuby
Bwa-mem2
cd-hit
CheckM
DAS
Diamond
eggNOG-mapper v2
MetaBAT 2
Minimap2
MMseqs
MultiQC
Pandas
Picard
pyfastx
SAMtools
SemiBin
Snakemake
SPAdes
SqueezeMeta
TADpole
VAMB
CONCOCT
ete3
gtdbtk
h5py
networkx
numpy
plotly
psutil
utils
metagenomics
Flexible workflow designed for bacterial WGS analyses (annotation, core/pan-genome reconstruction, phylogeny)
This pipeline is written specifically for annotating the bacteria whole genome sequences (WGS) . The pipeline handles mul...
The repository host the snakemake file for 16S rRNA and shotgun sequencing data including QIIME2 and kraken2/bracken for 16S and metaphalan3 and kraken2/bracken for shotgun.
This is an ongoing project to generate a snakemake workflow to anlaysis 16S rRNA and shotgun seqeucnign microbial data using ...
Twist Cancer hydragenetics pipeline for HG38
This pipeline is created to run on Illumina data from a custom Twist Inherited Cancer panel, designed at Clinical Genomics Up...
Snakemake workflow to analyse hematological malignancies in whole genome data
Snakemake workflow to analyse hematological malignancies in whole genome data This snakemake workflow uses modules from hydra...
MoMofy: Module for integrative Mobilome prediction
Module for integrative Mobilome prediction Bacteria can acquire genetic material through horizontal gene transfer, allowing t...