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SCAPP: an algorithm for improved plasmid assembly in metagenomes.

David PellowAlvah ZoreaMaraike ProbstOri FurmanArik SegalItzhak MizrahiRon Shamir
Published in: Microbiome (2021)
SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP . Video abstract.
Keyphrases
  • escherichia coli
  • crispr cas
  • endothelial cells
  • antibiotic resistance genes
  • machine learning
  • deep learning
  • klebsiella pneumoniae
  • wastewater treatment
  • neural network