Erratum: Toward perfect reads: Self-correction of short reads via mapping on de Bruijn graphs (Bioinformatics (2019) DOI: 10.1093/bioinformatics/btz102)

Abstract

Several corrections have been made to the above article. • In the article abstract, the word 'read' has been replaced by the word 'sequence.' • The caption for figure 1 has been replaced with the following text: 'Four issues with k-mer-spectrum methods, and how Bcool handles them (blue half-arrows represent the paths of the graph on which given reads map). (1) Genomic k-mers may be appear weak because of their low abundance: by using a very low k-mer abundance threshold coupled with a unitig abundance threshold, Bcool retains low-abundance k-mers and manages to correct the reads that contain them. (2) Erroneous k-mers may appear solid because of their high abundance: Bcool detects the tip pattern produced by such solid erroneous k-mers and is therefore able to discard them (other erroneous k-mers are detected at the unitig filtering step). (3) Sequencing errors may be validated by genomic k-mers originating from other parts of the genome: by considering mappings globally, Bcool chooses the best path for each read, i.e. The one on which it maps with the smallest number of mismatches. (4) Multiple errors may occur on a k-mer, resulting in a large weak region: by using unitigs instead of k-mers to correct reads, Bwise is able to correct properly reads that contain several nearby errors' • On page 3 of the PDF, 'k-mers' has been replaced with 'kvalues.' • On page 5 of the PDF the 'correction ratio' has been corrected from '= (TP + FN)/(FN + TP)' to '= (TP + FN)/(FN + FP)' • The following sentence has been added to the Figure 6 caption: 'BFC and Musket ran out of memory an all full human datasets' • The reference given for 'Limasset, A. et al. (2017)' has been corrected to the following: Limasset, A. et al. (2017) Fast and Scalable Minimal Perfect Hashing for Massive Key Sets. In: Iliopolis, C.S. et al. (eds) Proceedings of the 16th International symposium on Experimental Algorithms (SEA 2017), London, UK, June 21-23, 2017, Leibniz International Proceedings in informatics Volume 75, Schloss Dagstuhl-Leibniz-Zentrum für Informatik GmbH, Dagstuhl Publishing, Saarbrücken/Wadern, Germany, pp. 25: 1-25:16. The publisher apologises for these errors which have now been corrected.