Skip to main content
All data types Biochemistry data Drug discovery data Genomics & transcriptomics data Health data Imaging data Other data Protein data Public health data Serology data Social science and humanities data
Data Highlights
COVID Symptom Study Sweden (Partner) COVID-19 publication overview CRUSH Covid Uppsala (Partner) Multi-disease serology National Pandemic Centre (Historic) Post COVID-19 condition Register-based vaccination (RECOVAC) SARS-CoV-2 whole genome sequencing (Region Uppsala) Serology tests for SARS-CoV-2 at SciLifeLab Vaccine administration: COVID-19 Wastewater-based epidemiology
Funding opportunities Ongoing research projects Register-based research Swedish COVID-19 Publications
Emerging Pathogens SciLifeLab PLP Preparedness Resources
Research Data Management
Sample Collection Database
Antibiotic resistance COVID-19 Enteric viruses Infectious diseases Influenza Mpox
Editorials
Events & Training

Highly parallelised multi-taxonomic profiling of shotgun metagenomic data (nf-core/taxprofiler)

Highly parallelised multi-taxonomic profiling of shotgun metagenomic data (nf-core/taxprofiler)


Funding given for project project entitled:

Joint contributions from 3 PLP projects: Rapid establishment of comprehensive laboratory pandemic preparedness – RAPID-SEQ (PLP1 capability), Genomic Pandemic Preparedness Portfolio (G3P) (PLP1 capability), and Next generation clinical virology (PLP TDP project).

PI(s)/Head responsible for the resource:

Jan Albert (RAPID-SEQ), Valtteri Wirta (G3P), Tobias Allander (Next generation clinical virology)

Host organisation(s):

nf-core/taxprofiler is an international initiative within nf-core community and Swedish contributions from Karolinska Institutet, Karolinska University Hospital, SciLifeLab, Region Östergötland and Genomic Medicine Sweden.

Resource description:

A pipeline for taxonomic profiling of shotgun metagenomic data. The first stable release is publicly available.

The pipeline supports metagenomic data generated both from Illumina and Nanopore sequencing technology. It performs in-parallel taxonomic profiling with multiple taxonomic classifiers against multiple databases and produces standardised output tables. In addition, it performs quality control and optional read pre-processing (adapter trimming, low-complexity filtering and host read removal).

The pipeline is written in Nextflow DSL-2 workflow manager and it uses Docker/Singularity containers.

For more information on the Pandemic Laboratory Preparedness resources associated with this subproject, see Genomic Pandemic Preparedness Portfolio (G3P), Rapid establishment of comprehensive laboratory pandemic preparedness – RAPID-SEQ, and Next generation clinical virology. Please also refer to other associated subprojects; GMS Arctic and SC2 Reporter.

How this resource can be used for Pandemic Preparedness research:

The development version of the pipeline is already publicly available for taxonomic classification of metagenomic data and it can be used for Pandemic Preparedness research as soon as the first stable release is available.

Who and under which conditions is able to access the resource:

The nf-core/taxprofiler is open-source pipeline.

Available data, code, and protocols from the resource:

All code related to the pipeline for taxprofiler is available on GitHub.

SOPs, guidelines, publications, etc. describing the resource:

Instructions about how to use the pipeline are available on nf-core.

Webpage:

https://nf-co.re/taxprofiler/1.1.2

Contact information:

Sofia Stamouli
Bioinformatician
Email: sofia.stamouli@scilifelab.se