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Correction: HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes

BMC Bioinformatics volume 26, Article number: 43 (2025) Cite this article

The Original Article was published on 17 May 2023

Correction :BMC Bioinformatics (2023) 24:204 https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12859-023-05335-8


Following the publication of the original article [1], the authors would like to add new paragraphs that describes the new created software tool. The changes have been highlighted in bold typeface.


Background:


An example dataset is also provided to allow users to test the workflow on their systems. Due to changes made to Snakemake and to improve portability, we have additionally rewritten the workflow in Nextflow with the use of Apptainer for software redistribution. This solely requires a user to install a conda distribution, Nextflow and Apptainer.


AgRenSeq:


Read trimming


Illumina RenSeq reads of the diversity panel provided by the user are pre-processed with fastp version 0.23.2 using default options [18]. Reads that have already been trimmed and quality filtered experience minimal data loss. Fastp has been replaced with cutadapt in the Nextflow release to improve trimming consistency.


k-mer counting and aggregation:


For each set of RenSeq reads, k-mers are counted via Jellyfish version 2.2.10 count [19] with options -C -m 51 -s 1G -t 4. A tab-delimited dump file is created using jellyfish dump with options -L 10 -ct. Dump file paths are aggregated into a single file as a prerequisite for the AgRenSeq k-mer presence/absence matrix creation. The created matrix contains presence and absence scores for the identified k-mers in each sample. Jellyfish has been replaced with kmc in the Nextflow release as this improved efficiency.

Conclusions:

Our modification of dRenSeq to only assess regions covered by bait sequences also reduces the risk of false negatives caused by part of a gene, perhaps separated by a large intron, being absent in the enriched short reads. Due to changes made within Snakemake, active development of the workflow has moved to a Nextflow instance. This has an additional benefit of utilising Apptainer software containers to improve the efficiency and reproducability of software environment creation.


Availability:


Project Name: HISS. Latest re-implementation in Nextflow: https://github.com/Hutton-Potato-Genetics/nfHISS. Legacy Snakemake repository. Project homepage: https://github.com/SwiftSeal/HISS.

Reference

  1. Adams, et al. BMC Bioinformatics (2023) HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly. AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes. 2023;24:204. https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12859-023-05335-8.

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Authors and Affiliations

  1. Department of Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, DD2 5DA, UK

    Thomas M. Adams, Moray Smith & Ingo Hein

  2. School of Biology, University of St Andrews, St Andrews, KY16 9ST, UK

    Moray Smith

  3. Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK

    Yuhan Wang, Lynn H. Brown & Ingo Hein

  4. Department of Information and Computational Sciences, The James Hutton Institute, Invergowrie, DD2 5DA, UK

    Micha M. Bayer

Authors
  1. Thomas M. Adams
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  2. Moray Smith
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  3. Yuhan Wang
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  4. Lynn H. Brown
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  5. Micha M. Bayer
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  6. Ingo Hein
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Contributions

TMA developed the workfows for SMRT-RenSeq Assembly; MS developed the workfow for AgRenSeq; TMA, YW and LHB developed the workfow for dRenSeq; TMA and MS reviewed the code and contents of the Github repository; MB initially automated the dRenSeq and AgRenSeq approaches; TMA and MS drafted the manuscript; MB and IH conceived the integration of dRenSeq in the workfow and substantively revised the manuscript; IH provided the biological material for the study; all authors reviewed and approved the fnal manuscript.

Corresponding authors

Correspondence to Thomas M. Adams or Ingo Hein.

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Adams, T.M., Smith, M., Wang, Y. et al. Correction: HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes. BMC Bioinformatics 26, 43 (2025). https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12859-024-06014-y

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  • DOI: https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12859-024-06014-y

BMC Bioinformatics

ISSN: 1471-2105

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