All Published Workflows
20 workflows that have been reviewed and published
Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set
This is the code for a re-analysis of a [GEO dataset][1] that I
originally analyzed for [this paper][2] using statistical met...
BSgenome.Hsapiens.UCSC.hg19
BSgenome.Hsapiens.UCSC.hg38
Gene ID
Peak calling
Quality control report
macs2
ucsc-liftover
BEDTools
BiocParallel
Bowtie 2
csaw
Cufflinks
GenomicAlignments
GenomicRanges
GLUE
graphite
GSEABase
HISAT2
kallisto
Quant
rtracklayer
Salmon
SAMtools
Snakemake
SRAdb
STAR
SummarizedExperiment
assertthat
dplyr
forcats
future
getopt
ggforce
ggplot2
here
ks
magrittr
optparse
reshape2
rex
rlang
scales
stringr
rpy2
rctutils
ChIP-seq
A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets
A Snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB) data (and other custom benchm...
Snakemake workflow for the mapping and quantification of miRNAs and isomiRs from miRNA-Seq libraries.
MIRFLOWZ is a [Snakemake][snakemake] workflow for mapping miRNAs and isomiRs.
Installation
Cloning the repos...
Workflow module for metagenome assembly
A Snakemake workflow for metagenome assembly using metaspades and metahit. It does pre-assembly merging and read-correction i...
Houses a snakemake workflow used for multiple sequence alignment and maximum likelihood phylogeny construction of genes or proteins. Originally used to study sex determination genes in mosquitoes.
This snakemake file contains a workflow allowing the creation of MAFFT alignments and RAxML phylogenies. Inputs can either be...
Created for testing the metabolomics pipeline through snakemake
This is the Snakemake implementation of the pyOpenMS workflow tailored by Eftychia Eva Kontou and Axel Walter ...
Shotgun metagenomic sequencing processing pipeline
Snakemake
Apptainer/Singularity : while in many cases we do provide conda envs the only method of execution we...
Gene ID
Gene prediction
Gene report
ABRicate
AMRFinderPlus
antismash-lite
bracken
hmmer
antiSMASH
BBMap
Bowtie 2
cloudSPAdes
CoverM
dbCAN2
FastQC
humann
kraken2
Krona
MetaErg
MetaPhlAn
MetaQUAST
metaspades
MetaWRAP
plasmidspades
QUAST
rnaspades
SAMtools
seqkit
Snakemake
SortMeRNA
SPAdes
RGI
Metagenomic sequencing
process aligned isoseq libraries to: 1. identify consensus gene models ; 2. compare gene model maintenance between samples
This is a Snakemake project template. The Snakefile is under workflow .
Slides describing and justifying the use ...
Use Public Resources to answer a biological question
How to access genomic resource via its Python API
How to access image resource via its Python API
Relate image data to ...
Pox Virus Illumina Amplicon Workflow for half-genomes sequencing data
This workflow generates consensus sequences from Illumina PE-sequenced ARTIC data of pox virus samples.
It requires that all ...
VGP hybrid scaffolding with Bionano optical maps
Performs scaffolding using Bionano Data. Part of VGP assembly pipeline.
VGP purge assembly with purge_dups pipeline
Purge Phased assembly of duplications and overlaps. Include purge steps for Primary and Alternate assemblies.