Teams: Cimorgh IT solutions
Organizations: cimorgh IT
Expertise: Bioinformatics, Genomics, Metagenomics, Microbiology, NGS, Python, R, bash, WDL
Tools: Mathematical Modelling, R, WDL
Expertise: Bioinformatics, Genomics, Scientific workflow developement
Expertise: Bioinformatics, Genomics, Machine Learning
Tools: Python, R, Machine Learning
I am a Ph.D. student in Gong lab. I am interested in cancer genomics, including the mining of genetic risk determinants in cancer, functional prediction of genetic variants, tumor-associated molecular epidemiology, large-scale data integration, analysis, and mining, as well as the construction of bioinformatical data platforms.
Teams: Galaxy Training Network
Organizations: Erasmus University Medical Centre

Expertise: Genomics, amplicon analysis, Microbiology
Tools: Galaxy
Post-doc at ErasmusMC, Galaxy Training Network (GTN) Lead
Expertise: Bioinformatics, Genomics, Metagenomics, Data Management
Tools: CWL, Jupyter notebook, Nextflow, Molecular Biology, Workflows, Microbiology, Transcriptomics, Perl, Python, R
Expertise: Bioinformatics, Computer Science, Data Management, Genetics, Genomics, Machine Learning, Metagenomics, NGS, Scientific workflow developement, Software Engineering
Tools: Databases, Galaxy, Genomics, Jupyter notebook, Machine Learning, Nextflow, nf-core, PCR, Perl, Python, R, rtPCR, Snakemake, Transcriptomics, Virology, Web, Web services, Workflows
Dad, husband and PhD. Scientist, technologist and engineer. Bibliophile. Philomath. Passionate about science, medicine, research, computing and all things geeky!
Teams: MAB - ATGC
Organizations: Centre National de la Recherche Scientifique (CNRS)

Expertise: Bioinformatics, Genomics, algorithm, Machine Learning, Metagenomics, NGS, Computer Science
Tools: Transcriptomics, Genomics, Python, C/C++, Web services, Workflows
ERGA Protein-coding gene annotation workflow.
Adapted from the work of Sagane Joye:
https://github.com/sdind/genome_annotation_workflow
Prerequisites
The following programs are required to run the workflow and the listed version were tested. It should be noted that older versions of snakemake are not compatible with newer versions of singularity as is noted here: https://github.com/nextflow-io/nextflow/issues/1659.
conda v 23.7.3
...
CLAWS (CNAG's Long-read Assembly Workflow in Snakemake)
Snakemake Pipeline used for de novo genome assembly @CNAG. It has been developed for Snakemake v6.0.5.
It accepts Oxford Nanopore Technologies (ONT) reads, PacBio HFi reads, illumina paired-end data, illumina 10X data and Hi-C reads. It does the preprocessing of the reads, assembly, polishing, purge_dups, scaffodling and different evaluation steps. By default it will preprocess the reads, run Flye + Hypo + purge_dups + yahs and evaluate ...
Type: Snakemake
Creators: Jessica Gomez-Garrido, Fernando Cruz (CNAG), Francisco Camara (CNAG), Tyler Alioto (CNAG)
Submitter: Jessica Gomez-Garrido
ARA (Automated Record Analysis) : An automatic pipeline for exploration of SRA datasets with sequences as a query
Requirements
-
Docker
-
Please checkout the Docker installation guide.
or
-
Mamba package manager
-
Please checkout the mamba or micromamba official installation guide.
-
We prefer
mamba
overconda
since it is faster and uses ...
prepareChIPs
This is a simple snakemake
workflow template for preparing single-end ChIP-Seq data.
The steps implemented are:
- Download raw fastq files from SRA
- Trim and Filter raw fastq files using
AdapterRemoval
- Align to the supplied genome using
bowtie2
- Deduplicate Alignments using
Picard MarkDuplicates
- Call Macs2 Peaks using
macs2
A pdf of the rulegraph is available here
Full details for each step are given below. Any additional ...
A CWL-based pipeline for calling small germline variants, namely SNPs and small INDELs, by processing data from Whole-genome Sequencing (WGS) or Targeted Sequencing (e.g., Whole-exome sequencing; WES) experiments.
On the respective GitHub folder are available:
- The CWL wrappers and subworkflows for the workflow
- A pre-configured YAML template, based on validation analysis of publicly available HTS data
Briefly, the workflow performs the following steps:
- Quality control of Illumina reads ...
Type: Common Workflow Language
Creators: Konstantinos Kyritsis, Nikolaos Pechlivanis, Fotis Psomopoulos
Submitter: Konstantinos Kyritsis
A CWL-based pipeline for calling small germline variants, namely SNPs and small INDELs, by processing data from Whole-genome Sequencing (WGS) or Targeted Sequencing (e.g., Whole-exome sequencing; WES) experiments.
On the respective GitHub folder are available:
- The CWL wrappers and subworkflows for the workflow
- A pre-configured YAML template, based on validation analysis of publicly available HTS data
Briefly, the workflow performs the following steps:
- Quality control of Illumina reads ...
Type: Common Workflow Language
Creators: Konstantinos Kyritsis, Nikolaos Pechlivanis, Fotis Psomopoulos
Submitter: Konstantinos Kyritsis
MoMofy
Module for integrative Mobilome prediction
Bacteria can acquire genetic material through horizontal gene transfer, allowing them to rapidly adapt to changing environmental conditions. These mobile genetic elements can be classified into three main categories: plasmids, phages, and integrons. Autonomous elements are those capable of excising themselves from the chromosome, reintegrating elsewhere, and potentially modifying the host's physiology. Small integrative elements like insertion ...
IGVreport-nf
- Description
- Diagram
- User guide
- Workflow summaries
- Metadata
- Component tools
- Required (minimum) inputs/parameters
- Additional notes
- Help/FAQ/Troubleshooting
- Acknowledgements/citations/credits
Description
Quickly generate [IGV .html
...
GermlineStructuralV-nf
:wrench: This pipeline is currently under development :wrench:
- Description
- Diagram
- User guide
- Infrastructure usage and recommendations
- Benchmarking
- Workflow summaries
- Metadata
- Component tools
- Additional notes
- Help/FAQ/Troubleshooting
...
Type: Nextflow
Creators: Georgina Samaha, Marina Kennerson, Tracy Chew, Sarah Beecroft
Submitter: Georgina Samaha
IndexReferenceFasta-nf
===========
Workflow for Metagenomics from bins to metabolic models (GEMs)
Summary
- Prodigal gene prediction
- CarveMe genome scale metabolic model reconstruction
- MEMOTE for metabolic model testing
- SMETANA Species METabolic interaction ANAlysis
Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default
All tool CWL files and other workflows can be found here: Tools: https://gitlab.com/m-unlock/cwl Workflows: https://gitlab.com/m-unlock/cwl/workflows
**How ...
Workflow for LongRead Quality Control and Filtering
- NanoPlot (read quality control) before and after filtering
- Filtlong (read trimming)
- Kraken2 taxonomic read classification before and after filtering
- Minimap2 read filtering based on given references
Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default
All tool CWL files and other workflows can be found here: https://gitlab.com/m-unlock/cwl/workflows
**How to setup and use an UNLOCK ...
Type: Common Workflow Language
Creators: Bart Nijsse, Jasper Koehorst, Germán Royval
Submitter: Bart Nijsse
- Deprecated -
See our updated hybrid assembly workflow: https://workflowhub.eu/workflows/367
And other workflows: https://workflowhub.eu/projects/16#workflows
Workflow for sequencing with ONT Nanopore data, from basecalled reads to (meta)assembly and binning
- Workflow Nanopore Quality
- Kraken2 taxonomic classification of FASTQ reads
- Flye (de-novo assembly)
- Medaka (assembly polishing)
- metaQUAST (assembly quality reports)
When Illumina reads are provided:
- Workflow ...
Type: Common Workflow Language
Creators: Bart Nijsse, Jasper Koehorst, Germán Royval
Submitter: Jasper Koehorst
Workflow for Illumina Quality Control and Filtering
Multiple paired datasets will be merged into single paired dataset.
Summary:
- FastQC on raw data files
- fastp for read quality trimming
- BBduk for phiX and (optional) rRNA filtering
- Kraken2 for taxonomic classification of reads (optional)
- BBmap for (contamination) filtering using given references (optional)
- FastQC on filtered (merged) data
Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default ...
Bootstrapping-for-BQSR @ NCI-Gadi is a pipeline for bootstrapping a variant resource to enable GATK base quality score recalibration (BQSR) for non-model organisms that lack a publicly available variant resource. This implementation is optimised for the National Compute Infrastucture's Gadi HPC. Multiple rounds of bootstrapping can be performed. Users can use Fastq-to-bam @ NCI-Gadi and Germline-ShortV @ NCI-Gadi to ...
Local Cromwell implementation of GATK4 germline variant calling pipeline
See the GATK website for more information on this toolset
Assumptions
- Using hg38 human reference genome build
- Running 'locally' i.e. not using HPC/SLURM scheduling, or containers. This repo was specifically tested on Pawsey Nimbus 16 CPU, 64GB RAM virtual machine, primarily running in the
/data
volume storage partition. - Starting from short-read Illumina paired-end fastq ...
Fastq-to-BAM @ NCI-Gadi is a genome alignment workflow that takes raw FASTQ files, aligns them to a reference genome and outputs analysis ready BAM files. This workflow is designed for the National Computational Infrastructure's (NCI) Gadi supercompter, leveraging multiple nodes on NCI Gadi to run all stages of the workflow in parallel, either massively parallel using the scatter-gather approach or parallel by sample. It consists of a number of stages and follows the BROAD Institute's best practice ...
Type: Shell Script
Creators: Cali Willet, Tracy Chew, Georgina Samaha, Rosemarie Sadsad, Andrey Bliznyuk, Ben Menadue, Rika Kobayashi, Matthew Downton, Yue Sun
Submitter: Georgina Samaha
SLURM HPC Cromwell implementation of GATK4 germline variant calling pipeline
See the GATK website for more information on this toolset
Assumptions
- Using hg38 human reference genome build
- Running using HPC/SLURM scheduling. This repo was specifically tested on Pawsey Zeus machine, primarily running in the
/scratch
partition. - Starting from short-read Illumina paired-end fastq files as input
Dependencies
The following versions have been ...
Germline-ShortV @ NCI-Gadi is an implementation of the BROAD Institute's best practice workflow for germline short variant discovery. This implementation is optimised for the National Compute Infrastucture's Gadi HPC, utilising scatter-gather parallelism to enable use of multiple nodes with high CPU or memory efficiency. This workflow requires sample BAM files, which can be generated using the Fastq-to-bam @ NCI-Gadi pipeline. Germline-ShortV can be applied ...
Type: Shell Script
Creators: Rosemarie Sadsad, Georgina Samaha, Tracy Chew, Cali Willet
Submitter: Tracy Chew
ORSON combine state-of-the-art tools for annotation processes within a Nextflow pipeline: sequence similarity search (PLAST, BLAST or Diamond), functional annotation retrieval (BeeDeeM) and functional prediction (InterProScan). When required, BUSCO completness evaluation and eggNOG Orthogroup annotation can be activated. While ORSON results can be analyzed through the command-line, it also offers the possibility to be compatible with BlastViewer or Blast2GO graphical tools.
Type: Nextflow
Creators: Cyril Noel, Alexandre Cormier, Patrick Durand, Laura Leroi, Pierre Cuzin
Submitter: Patrick Durand
Collection of de-novo genome assembly workflows written for implementation in Galaxy
Input data should be PacBio HiFi reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads
Executing all workflows will output two, scaffolded, haplotype assemblies
Maintainers: Tom Brown, Diego De Panis
Number of items: 6
Tags: Assembly, Bioinformatics, Galaxy, Genomics, ONT, Genome assembly, HiFi
The Vertebrate Genomes Pipelines in Galaxy are intended to allow a user to generate high-quality near error-free assemblies of species from a user's own data or from the GenomeArk database.