<?xml version="1.0" encoding="utf-8" standalone="yes"?><feed xmlns="http://www.w3.org/2005/Atom"><generator uri="https://gohugo.io" version="0.141.0">Hugo v0.141.0</generator><id>https://millironx.millironx.page/@indiewebpub/people/sofia-stamouli/</id><link rel="self" type="application/atom+xml" href="https://millironx.millironx.page/@indiewebpub/people/sofia-stamouli/feed.xml"/><link rel="alternate" type="text/html" href="https://millironx.millironx.page/@indiewebpub/people/sofia-stamouli/"/><updated>2025-03-31T00:14:19+00:00</updated><title>Sofia Stamouli's activity on Milliron X</title><entry><id>https://millironx.millironx.page/@indiewebpub/academia/taxprofiler/</id><link rel="alternate" href="https://doi.org/10.1101/2023.10.20.563221"/><title>nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling</title><published>2023-10-23T00:00:00+00:00</published><updated>2023-10-23T00:00:00+00:00</updated><author><name>Sofia Stamouli</name><uri>https://millironx.millironx.page/@indiewebpub/people/sofia-stamouli/</uri></author><author><name>Moritz E. Beber</name><uri>https://millironx.millironx.page/@indiewebpub/people/moritz-e.-beber/</uri></author><author><name>Tanja Normark</name><uri>https://millironx.millironx.page/@indiewebpub/people/tanja-normark/</uri></author><author><name>Thomas A. Christensen II</name><uri>https://millironx.millironx.page/@indiewebpub/people/thomas-a.-christensen-ii/</uri></author><author><name>Lili Andersson-Li</name><uri>https://millironx.millironx.page/@indiewebpub/people/lili-andersson-li/</uri></author><author><name>Maxime Borry</name><uri>https://millironx.millironx.page/@indiewebpub/people/maxime-borry/</uri></author><author><name>Mahwash Jamy</name><uri>https://millironx.millironx.page/@indiewebpub/people/mahwash-jamy/</uri></author><author><name>Nf-Core Community</name><uri>https://millironx.millironx.page/@indiewebpub/people/nf-core-community/</uri></author><author><name>James A. Fellows Yates</name><uri>https://millironx.millironx.page/@indiewebpub/people/james-a.-fellows-yates/</uri></author><category term="paper"/><category term="genomics"/><summary type="text">
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.</summary><content type="html" xml:lang="en" xml:base="https://millironx.millironx.page/@indiewebpub/">
&lt;p>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.&lt;/p>
</content></entry></feed>