{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T06:15:56Z","timestamp":1788156956280,"version":"build-2803163510"},"reference-count":22,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T00:00:00Z","timestamp":1788134400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>\n                      Repeatome characterization from short-read sequencing data is widely performed using RepeatExplorer2\/TAREAN. However, long-lived multisample projects and explicit comparative designs are often executed as\n                      <jats:italic>ad hoc<\/jats:italic>\n                      command sequences that are hard to version, rerun, and monitor on shared compute environments \u2014 a gap that motivates a project-centric workflow layer for repeatome analysis.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      We present REAPER (Repeatome Extended Analysis Pipeline\u2014Execution and Reporting), a project-centric workflow layer that couples a modular Snakemake pipeline with a Python project manager to enforce a stable on-disk layout and configuration-driven execution for single-sample and comparative repeatome analyses. REAPER does not implement a new repeat-discovery algorithm; it is an orchestration layer, and biological accuracy for clustering and satellite calling depends on the underlying RepeatExplorer2\/TAREAN and satMiner methods it coordinates. REAPER standardizes: Read QC Deterministic subsampling and preparation RepeatExplorer2\/TAREAN execution via seqclust, with satMiner-inspired iterative assembly Post-TAREAN BLAST-based annotation against curated repeat collections (optionally including taxon-scoped NCBI-derived resources with freshness checks) Optional graph-based comparative reports The pipeline makes comparative read allocation, prefix policy, and analysis-ready tables explicit; caching supports incremental reruns and structured logs support monitoring. Performance was assessed using a\n                      <jats:italic>Triticeae<\/jats:italic>\n                      short-read dataset (five samples), with rule-level logging of runtime and memory across pipeline stages.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Rule-level performance logs show that graph-based clustering dominates runtime and memory, while QC and preparation steps are lightweight by comparison. Graph-report annotations for the Triticeae project additionally link high-ranking clusters to established repeat markers \u2014 including pTa794- and pSc119-class entries in curated databases.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>\n                      These findings illustrate biologically interpretable outputs (recovery of known\n                      <jats:italic>Triticeae<\/jats:italic>\n                      repeat markers) alongside quantitative performance metrics (identification of graph-based clustering as the dominant computational cost). By making comparative read allocation, prefix policy, and analysis-ready tables explicit \u2014 and by supporting caching and structured logging \u2014 REAPER supports reproducible comparative repeatome analysis in evolving multisample projects. As an orchestration layer rather than a discovery algorithm, REAPER's contribution lies in reproducibility, monitorability, and comparative-analysis infrastructure, with biological accuracy remaining contingent on the underlying RepeatExplorer2\/TAREAN and satMiner methods.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fpls.2026.1855960","type":"journal-article","created":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T05:41:23Z","timestamp":1788154883000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["REAPER: a project-centric workflow layer for comparative repeatome analysis"],"prefix":"10.3389","volume":"17","author":[{"given":"Daniil S.","family":"Ulyanov","sequence":"first","affiliation":[{"name":"All-Russia Research Institute of Agricultural Biotechnology","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna I.","family":"Yurkina","sequence":"additional","affiliation":[{"name":"All-Russia Research Institute of Agricultural Biotechnology","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Viktoria S.","family":"Voronezhskaya","sequence":"additional","affiliation":[{"name":"All-Russia Research Institute of Agricultural Biotechnology","place":["Moscow, Russia"]},{"name":"School of Biological and Medical Physics, Moscow Institute of Physics and Technology","place":["Dolgoprudny, Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alana A.","family":"Ulyanova","sequence":"additional","affiliation":[{"name":"All-Russia Research Institute of Agricultural Biotechnology","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pavel Yu.","family":"Kroupin","sequence":"additional","affiliation":[{"name":"All-Russia Research Institute of Agricultural Biotechnology","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mikhail G.","family":"Divashuk","sequence":"additional","affiliation":[{"name":"All-Russia Research Institute of Agricultural Biotechnology","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,31]]},"reference":[{"key":"B1","unstructured":"FastQC a quality control tool for high throughput sequence data\n          \n          2010"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1186\/s13100-015-0041-9","article-title":"Repbase update, a database of repetitive elements in eukaryotic genomes","volume":"6","author":"Bao","year":"2015","journal-title":"Mobile DNA"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0185056","article-title":"BBMerge \u2013 accurate paired shotgun read merging via overlap","volume":"12","author":"Bushnell","year":"2017","journal-title":"PLoS One"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinf."},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evac064","article-title":"In-depth satellitome analyses of 37 Drosophila species illuminate repetitive DNA evolution in the Drosophila genus","volume":"14","author":"De Lima","year":"2022","journal-title":"Genome Biol. 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