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Automated Robotic Liquid Handling Assembly of Modular DNA Devices
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Plastaumatic: Automating plastome assembly and annotation.

Wenyi Chen1, Sai Reddy Achakkagari1, Martina Strömvik1

  • 1Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada.

Frontiers in Plant Science
|November 21, 2022
PubMed
Summary
This summary is machine-generated.

This study introduces Plastaumatic, an automated pipeline that simplifies the assembly and annotation of plant plastome sequences. It significantly reduces manual input and processing time for researchers working with multiple genomes.

Keywords:
chloroplast genomeorganellar genomeplantplastomesequence assembly

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Area of Science:

  • Plant genomics
  • Bioinformatics

Background:

  • Plastome sequence data requires separate assembly and annotation from nuclear genomes.
  • Manual processing of multiple plastomes is labor-intensive and time-consuming.

Purpose of the Study:

  • To develop an automated pipeline, Plastaumatic, for efficient plastome assembly and annotation.
  • To minimize manual input and accelerate the processing of whole genome sequence data for plastomes.

Main Methods:

  • The Plastaumatic pipeline integrates trimming (fastp), de novo assembly (NOVOPlasty), quality control (BLAST+, SAMtools), and annotation (AnnoPlast).
  • It automates the generation of files for NCBI GenBank submission.

Main Results:

  • Plastaumatic was successfully demonstrated on 12 potato and 3 soybean accessions.
  • The pipeline streamlines the workflow for plastome data analysis.

Conclusions:

  • Plastaumatic offers a faster and more efficient solution for plastome assembly and annotation.
  • This tool is valuable for researchers analyzing large-scale plant genomic datasets.