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  • 1Center for Algorithmic Biotechnologies, Saint Petersburg State University, Saint Petersburg, Russia.

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|June 20, 2020
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Summary
This summary is machine-generated.

SPAdes is a versatile genome assembler for microbial, metagenomic, and transcriptomic data. This guide details five SPAdes pipelines for diverse assembly tasks, including plasmids and gene clusters, with usage instructions.

Keywords:
biosynthetic gene clustersde novo assemblygenome assemblymetagenomesplasmidstranscriptome

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • SPAdes (St. Petersburg genome Assembler) initially focused on de novo assembly for microbial isolates and single-cell sequencing.
  • Its capabilities expanded to include IonTorrent data and hybrid assembly using short and long reads (PacBio, Oxford Nanopore).

Purpose of the Study:

  • To present five distinct SPAdes assembly pipelines for various genomic datasets.
  • To provide protocols for assembling metagenomes, transcriptomes, plasmids, and biosynthetic gene clusters.
  • To offer guidelines and use cases for interpreting SPAdes assembly results.

Main Methods:

  • Detailed protocols for five SPAdes assembly pipelines: isolate bacteria, metagenomes, plasmids, transcriptomes, and biosynthetic gene clusters.
  • Support protocols covering installation, input methods (command line, YAML), run restarting, and strand-specificity determination.
  • Demonstration of SPAdes' utility across diverse sequencing data types and assembly challenges.

Main Results:

  • The SPAdes package offers comprehensive solutions for assembling various genomic data types.
  • The presented protocols facilitate efficient and accurate assembly of complex biological datasets.
  • Guidelines and use cases enhance the practical application and understanding of SPAdes outputs.

Conclusions:

  • SPAdes is a powerful and adaptable tool for a wide range of genome assembly applications.
  • The documented pipelines and support protocols empower researchers to effectively utilize SPAdes for microbial, metagenomic, and transcriptomic analyses.