First Phylogenetic Analysis of Malian SARS-CoV-2 Sequences Provides Molecular Insights into the Genomic Diversity of the Sahel Region

Article activity feed

1. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2020.09.23.20165639: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   After passing sequence quality control, demultiplexing requiring barcodes at both ends of the reads was achieved using Porechop [15] and adapter trimming was achieved by the ARTIC pipeline [13] setting Wuhan-Hu-1 as reference strain for read mapping.	Porechop suggested: (Porechop, RRID:SCR_016967)
   For this purpose, SARS-CoV-2 specific baits (myBaits Expert SARS-CoV-2, Arbor Sciences, BioCat, Heidelberg, Germany) were used according to the manufacturers’ instructions and captured …

   SciScore for 10.1101/2020.09.23.20165639: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   After passing sequence quality control, demultiplexing requiring barcodes at both ends of the reads was achieved using Porechop [15] and adapter trimming was achieved by the ARTIC pipeline [13] setting Wuhan-Hu-1 as reference strain for read mapping.	Porechop suggested: (Porechop, RRID:SCR_016967)
   For this purpose, SARS-CoV-2 specific baits (myBaits Expert SARS-CoV-2, Arbor Sciences, BioCat, Heidelberg, Germany) were used according to the manufacturers’ instructions and captured libraries were sequenced using Sequencing V2 Reagent chemistry 300 cycles on a Micro Flow Cell (Illumina Inc, Berlin, Germany)	BioCat suggested: (BioCAT, RRID:SCR_001440)
   The obtained bam files were added as a separate read-group to the bam files generated by the ARTIC pipeline using SAMtools [17].	SAMtools suggested: (SAMTOOLS, RRID:SCR_002105)
   Additionally, variants were called for the Illumina mapping using BCFtools v1.9-168 of the SAMtools package [17] and merged with the variant VCF files from the ARTIC pipeline, if necessary.	BCFtools suggested: (SAMtools/BCFtools, RRID:SCR_005227)

   ---

   Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

   ---

   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.

   ---

   Read the original source
2. Version published to 10.3390/v12111251

   Nov 2, 2020
3. 

   Version published to 10.1101/2020.09.23.20165639v1 on medRxiv

   Sep 25, 2020
4. 

   Version published to 10.1101/2020.09.23.20165639v2 on medRxiv

   Sep 25, 2020