Head of Bioinformatics Group, Center for Proteomics and Metabolomics, Leiden University Medical Center Interested in workflows and automated workflow composition for analysis of mass spectrometry data, in particular within proteomics or metabolomics, integration with genomics data and the scientific literature
Teams: V-pipe
Organizations: Swiss Institute of Bioinformatics
https://orcid.org/0000-0002-7561-0810
Teams: Seven Bridges Open Workflows
Organizations: Seven Bridges
https://orcid.org/0000-0003-2933-1260
I have a computer science background and I work in bioinformatics. I am interested in structural variant calling.
Research Engineer in Barcelona Supercomputing Center (BSC)
Projet de Hackathon du master AMI2B 2022 - Pipeline d'analyse RNA-Seq écrit en Nextflow
Type: Nextflow
Creators: George , George-Marchment , ClemenceS , ambrebaumann , Lindsay Goulet, Lindsay-Goulet , Ubuntu , Ambre , Lindsay GOULET
Submitter: George Marchment
Assembly, binning and annotation of metagenomes.
Introduction
This pipeline is for assembly, binning and annotation of metagenomes. It supports both short and long reads, quality trims the reads and adapters with https://github.com/OpenGene/fastp and https://github.com/rrwick/Porechop and performs basic QC with https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
The pipeline then:
assigns taxonomy to reads using https://ccb.jhu.edu/software/centrifuge/ and/or https://ccb.jhu.edu/software/kraken2/ ...
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