25 lines
1.7 KiB
Markdown
25 lines
1.7 KiB
Markdown
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---
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title:
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"nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling"
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date: 2023-10-23
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featured: true
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tags:
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- genomics
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categories:
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- paper
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people:
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- Sofia Stamouli
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- Moritz E. Beber
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- Tanja Normark
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- Thomas A. Christensen II
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- Lili Andersson-Li
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- Maxime Borry
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- Mahwash Jamy
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- nf-core community
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- James A. Fellows Yate
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link: https://doi.org/10.1101/2023.10.20.563221
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journal: bioRxiv
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---
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Metagenomic classification tackles the problem of characterising the taxonomic source of all DNA sequencing reads in a sample. A common approach to address the differences and biases between the many different taxonomic classification tools is to run metagenomic data through multiple classification tools and databases. This, however, is a very time-consuming task when performed manually - particularly when combined with the appropriate preprocessing of sequencing reads before the classification. Here we present nf-core/taxprofiler, a highly parallelised read-processing and taxonomic classification pipeline. It is designed for the automated and simultaneous classification and/or profiling of both short- and long-read metagenomic sequencing libraries against a 11 taxonomic classifiers and profilers as well as databases within a single pipeline run. Implemented in Nextflow and as part of the nf-core initiative, the pipeline benefits from high levels of scalability and portability, accommodating from small to extremely large projects on a wide range of computing infrastructure. It has been developed following best-practise software development practises and community support to ensure longevity and adaptability of the pipeline, to help keep it up to date with the field of metagenomics.
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