The Easy-to-Use SARS-CoV-2 Assembler for Genome Sequencing: Development Study
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Abstract
Early sequencing and quick analysis of the SARS-CoV-2 genome have contributed to the understanding of the dynamics of COVID-19 epidemics and in designing countermeasures at a global level.
Objective
Amplicon-based next-generation sequencing (NGS) methods are widely used to sequence the SARS-CoV-2 genome and to identify novel variants that are emerging in rapid succession as well as harboring multiple deletions and amino acid–changing mutations.
Methods
To facilitate the analysis of NGS sequencing data obtained from amplicon-based sequencing methods, here, we propose an easy-to-use SARS-CoV-2 genome assembler: the Easy-to-use SARS-CoV-2 Assembler (ESCA) pipeline.
Results
Our results have shown that ESCA could perform high-quality genome assembly from Ion Torrent and Illumina raw data and help the user in easily correct low-coverage regions. Moreover, ESCA includes the possibility of comparing assembled genomes of multisample runs through an easy table format.
Conclusions
In conclusion, ESCA automatically furnished a variant table output file, fundamental to rapidly recognizing variants of interest. Our pipeline could be a useful method for obtaining a complete, rapid, and accurate analysis even with minimal knowledge in bioinformatics.
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SciScore for 10.1101/2021.05.21.445156: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Sample preprocessing is performed filtering out all reads with mean Phred quality score lower than 20 and less than 30 nucleotides long. Phredsuggested: (Phred, RRID:SCR_001017)Genome coverage is then analyzed: read-mapping file is converted in “sorted-bam” and “mpileup” files using samtools software [16] and those data are translated in a detailed coverage table that reports the count of nucleotides observed at each position. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)The respectively results were compared … SciScore for 10.1101/2021.05.21.445156: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Sample preprocessing is performed filtering out all reads with mean Phred quality score lower than 20 and less than 30 nucleotides long. Phredsuggested: (Phred, RRID:SCR_001017)Genome coverage is then analyzed: read-mapping file is converted in “sorted-bam” and “mpileup” files using samtools software [16] and those data are translated in a detailed coverage table that reports the count of nucleotides observed at each position. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)The respectively results were compared aligning the sequences obtained with the two methods with the reference (Wuhan-Hu-1, NCBI Acc.Numb. NC_045512.2) and the corrected sequence submitted to GISAID, using MAFFT [19]. MAFFTsuggested: (MAFFT, RRID:SCR_011811)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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