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
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. https://doi.org/10.1093/bioinformatics/bts723
PMID: 23303509
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