ImmunoTyper-SR: A computational approach for genotyping immunoglobulin heavy chain variable genes using short-read data

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1. Version published to 10.1016/j.cels.2022.08.008

   Oct 1, 2022
2. 

   ScreenIT

   Feb 5, 2022

   SciScore for 10.1101/2022.01.31.478564: (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

   Antibodies
   Sentences	Resources
   2.5 Statistical Association between IGHV Genotype and anti-Type I IFN Autoantibody Presence: First, the 585 samples from the NIAID cohort were filtered for the presence of α, β, ω IFN autoantibody labels.	anti-Type I suggested: None
   Software and Algorithms
   Sentences	Resources
   2.2 Allele Candidate Assignment: The extracted reads are then mapped to a database of IGHV allele reference sequences using BWA-MEM[30], with the -a option.	BWA-MEM[30] suggested: None
   2.3.4 ILP Model Formulation: Definitions: Let be the set of all WGS reads in the sample.	WGS suggested: None
   The complete allele database was mapped against …

   SciScore for 10.1101/2022.01.31.478564: (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

   Antibodies
   Sentences	Resources
   2.5 Statistical Association between IGHV Genotype and anti-Type I IFN Autoantibody Presence: First, the 585 samples from the NIAID cohort were filtered for the presence of α, β, ω IFN autoantibody labels.	anti-Type I suggested: None
   Software and Algorithms
   Sentences	Resources
   2.2 Allele Candidate Assignment: The extracted reads are then mapped to a database of IGHV allele reference sequences using BWA-MEM[30], with the -a option.	BWA-MEM[30] suggested: None
   2.3.4 ILP Model Formulation: Definitions: Let be the set of all WGS reads in the sample.	WGS suggested: None
   The complete allele database was mapped against each assembly using Bowtie2[35] (with -af --end-to-end --very-fast parameters).	Bowtie2 suggested: (Bowtie 2, RRID:SCR_016368)

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   Results from OddPub: Thank you for sharing your code and data.

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   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.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   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.

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   Results from scite Reference Check: We found no unreliable references.

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3. 

   Version published to 10.1101/2022.01.31.478564 on bioRxiv

   Feb 2, 2022