Laura Rodriguez-Navas
Research Engineer in Barcelona Supercomputing Center (BSC)
SEEK ID: https://workflowhub.eu/people/4
Location:
Spain
Expertise: Software Engineering, Bioinformatics
Tools: Workflows, Machine Learning, Python
https://orcid.org/0000-0003-4929-1219
Their tagsRelated items
Ongoing analysis of COVID-19 using Galaxy, BioConda and public research infrastructures https://covid19.galaxyproject.org
Space: COVID-19 Biohackathon
Public web page: https://github.com/galaxyproject/SARS-CoV-2
MGnify (formerly known as EBImetagenomics) is a free resource for the assembly, analysis, archiving and browsing all types of microbiome derived sequence data.
Space: This Team is not associated with a Space
Public web page: Not specified
nfcore/viralrecon is a bioinformatics analysis pipeline used to perform assembly and intrahost/low-frequency variant calling for viral samples. The pipeline currently supports metagenomics and amplicon sequencing data derived from the Illumina sequencing platform.
Space: COVID-19 Biohackathon
Public web page: https://github.com/nf-core/viralrecon
Stable
VIRify
VIRify is a recently developed pipeline for the detection, annotation, and taxonomic classification of viral contigs in metagenomic and metatranscriptomic assemblies. The pipeline is part of the repertoire of analysis services offered by MGnify. VIRify’s taxonomic classification relies on the detection of taxon-specific profile hidden Markov models (HMMs), built upon a set of 22,014 orthologous protein domains and referred to as ViPhOGs.
A nextflow implementation of the VIRify pipeline for
...
Type: Nextflow
Creators: Martin Beracochea, Martín Beracochea, Martin Hölzer, Alexandre Almeida, Guillermo Rangel-Pineros and Ekaterina Sakharova
Submitter: Laura Rodriguez-Navas
Download
Stable
VIRify
VIRify is a recently developed pipeline for the detection, annotation, and taxonomic classification of viral contigs in metagenomic and metatranscriptomic assemblies. The pipeline is part of the repertoire of analysis services offered by MGnify. VIRify’s taxonomic classification relies on the detection of taxon-specific profile hidden Markov models (HMMs), built upon a set of 22,014 orthologous protein domains and referred to as ViPhOGs.
VIRify was implemented in CWL.
What do I need?
The
...
Type: Common Workflow Language
Creators: Martin Beracochea, Martín Beracochea, Martin Hölzer, Alexandre Almeida, Guillermo Rangel-Pineros and Ekaterina Sakharova
Submitter: Laura Rodriguez-Navas
Stable
nf-core/vipr is a bioinformatics best-practice analysis pipeline for assembly and intrahost / low-frequency variant calling for viral samples.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.
Pipeline Steps
Step
Main program/s
Trimming, combining of read-pairs per sample and QC
Skewer, FastQC
Decontamination
...
Type: Nextflow
Creator: Andreas Wilm and October SESSIONS and Paola Florez DE SESSIONS and ZHU Yuan and Shuzhen SIM and CHU Wenhan Collins
Submitter: Laura Rodriguez-Navas
