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Fig. 1 | BMC Bioinformatics

Fig. 1

From: NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads

Fig. 1

Path gap exclusion. The black line represents an assembly. The assembly regions marked by red colour correspond to repeated regions. The repeated regions are identical or near-identical copies of the same repeat or copies of different repeats. The arrows represent read paths. (a) Exclusion of a path gap fully covered by a read path of the same type and another orientation. The rectangles between read paths indicate path gaps. Path gap 1 is excluded due to the presence of a required read path. The path gaps marked by number 2 are not excluded and require further analysis. (b) Exclusion of a path gap appeared due to alternation of paths of different types. The black squares mark the locations of assembly errors. The rectangles between read paths indicate path gaps that are not excluded. The path gaps marked by number 3 is not excluded due to the repetition of read path types (e.g. the Single forward-oriented path is followed by another Single forward-oriented path instead of the Single-Multiple forward-oriented path). The path gaps marked by number 4 are not excluded because one read path type is missed (e.g. Multiple forward-oriented path is followed by Single forward-oriented path instead of Multiple-Single forward-oriented path)

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