Correction to: HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes (BMC Bioinformatics, (2023), 24, 1, (204), 10.1186/s12859-023-05335-8)

TY - JOUR

T1 - Correction to

T2 - HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes (BMC Bioinformatics, (2023), 24, 1, (204), 10.1186/s12859-023-05335-8)

AU - Adams, Thomas M.

AU - Smith, Moray

AU - Wang, Yuhan

AU - Brown, Lynn H.

AU - Bayer, Micha M.

AU - Hein, Ingo

N1 - Publisher Copyright: © The Author(s) 2025.

PY - 2025/2/7

Y1 - 2025/2/7

N2 - 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. 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.

AB - 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. 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.

UR - https://www.scopus.com/pages/publications/85218359120

U2 - 10.1186/s12859-024-06014-y

DO - 10.1186/s12859-024-06014-y

M3 - Comment/debate

C2 - 39920604

AN - SCOPUS:85218359120

SN - 1471-2105

VL - 26

JO - BMC Bioinformatics

JF - BMC Bioinformatics

IS - 1

M1 - 43

ER -