poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing
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Abstract
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 .
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SciScore for 10.1101/2021.05.07.443089: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources General mappings are performed with minimap2 (Li, 2018), and intermediate file transformations are performed with SAMtools and BCFtools (Danecek et al., 2021). SAMtoolssuggested: (SAMTOOLS, RRID:SCR_002105)Additionally, all reads for each sample are mapped back against the Wuhan reference genome (Accession: NC_045512.2) using BWA-MEM (Li, 2013) to provide visual feedback of amplicon drop-outs, which are a common issue during the multiplex PCR step of the tiled amplicon sequencing protocol. BWA-MEMsuggested: (Sniffles, RRID:SCR_017619)Results from OddPub: Thank you for sharing your code and …
SciScore for 10.1101/2021.05.07.443089: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources General mappings are performed with minimap2 (Li, 2018), and intermediate file transformations are performed with SAMtools and BCFtools (Danecek et al., 2021). SAMtoolssuggested: (SAMTOOLS, RRID:SCR_002105)Additionally, all reads for each sample are mapped back against the Wuhan reference genome (Accession: NC_045512.2) using BWA-MEM (Li, 2013) to provide visual feedback of amplicon drop-outs, which are a common issue during the multiplex PCR step of the tiled amplicon sequencing protocol. BWA-MEMsuggested: (Sniffles, RRID:SCR_017619)Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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