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Assembly Likelihood Evaluation (ALE) is a tool for evaluating accuracy of assemblies without the need of a reference genome. It makes use of read quality, mate pair orientation, insert length, sequencing coverage, read alignment and k-mer frequency. This tool can be used to detect errors in metagenomes as well by pinpointing single base errors, indels, genome re-arrangement and chimera.


Sequence assembly


  • Operation: Genome assembly evaluation
  • Software interface: command-line user interface
  • Language: C
  • Operating system: Linux
  • License: The University of Illinois/NCSA Open Source License
  • Cost: Free
  • Version name: -
  • Credit: U.S. Department of Energy
  • Contact: ZhongWang _at_
  • Collection: -


Clark SC, Egan R, Frazier PI, Wang Z "ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies." Bioinformatics. 2013 Feb 15;29(4):435-43. Epub 2013 Jan 9.
PMID: 23303509

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