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
https://orcid.org/0000-0003-3803-468X
Post-doc at ErasmusMC, Galaxy Training Network (GTN) Lead
Dad, husband and PhD. Scientist, technologist and engineer. Bibliophile. Philomath. Passionate about science, medicine, research, computing and all things geeky!
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
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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 ...
DownloadLocal 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
/datavolume 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
/scratchpartition. - 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
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.
