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<p><i>crocketa</i> (single-Cell Repertoire Organization &amp; Combined Kinetics Exploration for Transcriptomic Analysis) is an automated and adaptable <i>Snakemake</i> pipeline designed to perform fundamental initial stages of single-cell analysis for both transcriptomic and immune repertoire data, with additional steps for detailed assay characterization. <i>crocketa</i> stems from the imperative need to devise an optimal methodology for integrating and analyzing single-cell RNA sequencing (scRNA-seq) alongside single-cell T-cell Receptor (scTCR-seq) or B-Cell Receptor (scBCR-seq) data in an automated way by means of state-of-the-art tools. This pipeline encompasses basic steps from primary &amp; secondary scRNA-seq along with the incorporation and analysis of immune repertoire, capable of accommodating both human and mouse datasets. <i>crocketa</i> addresses this need by providing a reproducible and automated framework for integrated analysis of single-cell transcriptomic and immune-repertoire data.</p> Graphical Abstract <p></p>

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crocketa: an automated Snakemake framework for integrated single-cell transcriptome and immune-repertoire analysis

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年3月21日

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  • Gonzalo Soria-Alcaide,
  • Gonzalo García-Aguilera,
  • Marta Portasany-Rodríguez,
  • Jaanam Lalchandani,
  • África González-Murillo,
  • Elena G. Sánchez,
  • Cristina Saiz-Ladera,
  • Manuel Ramírez-Orellana,
  • Jorge Garcia-Martinez

摘要

crocketa (single-Cell Repertoire Organization & Combined Kinetics Exploration for Transcriptomic Analysis) is an automated and adaptable Snakemake pipeline designed to perform fundamental initial stages of single-cell analysis for both transcriptomic and immune repertoire data, with additional steps for detailed assay characterization. crocketa stems from the imperative need to devise an optimal methodology for integrating and analyzing single-cell RNA sequencing (scRNA-seq) alongside single-cell T-cell Receptor (scTCR-seq) or B-Cell Receptor (scBCR-seq) data in an automated way by means of state-of-the-art tools. This pipeline encompasses basic steps from primary & secondary scRNA-seq along with the incorporation and analysis of immune repertoire, capable of accommodating both human and mouse datasets. crocketa addresses this need by providing a reproducible and automated framework for integrated analysis of single-cell transcriptomic and immune-repertoire data.

Graphical Abstract