000K  utf8
1100  2021$c2021-07-28
1500  eng
2051  10.3389/fgene.2021.711437
3000  Brandt, Christian
3010  Hölzer, Martin
3010  Jundzill, Mateusz
3010  Krautwurst, Sebastian
3010  Lohde, Mara
3010  Marquet, Mike
3010  Spott, Riccardo
4000  poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing  [Brandt, Christian]
4060  8 Seiten
4209  In response to the SARS-CoV-2 pandemic, a highly increased sequencing effort has been established worldwide to track and trace ongoing viral evolution. Technologies, such as nanopore sequencing via the ARTIC protocol are used to reliably generate genomes from raw sequencing data as a crucial base for molecular surveillance. However, for many labs that perform SARS-CoV-2 sequencing, bioinformatics is still a major bottleneck, especially if hundreds of samples need to be processed in a recurring fashion. Pipelines developed for short-read data cannot be applied to nanopore data. Therefore, specific long-read tools and parameter settings need to be orchestrated to enable accurate genotyping and robust reference-based genome reconstruction of SARS-CoV-2 genomes from nanopore data. Here we present poreCov, a highly parallel workflow written in Nextflow, using containers to wrap all the tools necessary for a routine SARS-CoV-2 sequencing lab into one program. The ease of installation, combined with concise summary reports that clearly highlight all relevant information, enables rapid and reliable analysis of hundreds of SARS-CoV-2 raw sequence data sets or genomes. poreCov is freely available on GitHub under the GNUv3 license: github.com/replikation/poreCov .
4950  https://doi.org/10.3389/fgene.2021.711437$xR$3Volltext$534
4961  https://www.db-thueringen.de/receive/dbt_mods_00049433
5051  570
5550  bioinformatics
5550  coronavirus – COVID-19
5550  docker
5550  lineages
5550  nanopore sequencing
5550  Nextflow
5550  pipeline
5550  SARS-CoV-2