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Fig. 9 | Genome Biology

Fig. 9

From: Widespread false gene gains caused by duplication errors in genome assemblies

Fig. 9

False duplications and their correction in the VGP zebra finch assembly. a The NPNT gene in the VGP zebra finch v1.0 assembly bTaeGut1.0 (first release) has the NPNT-like gene adjacent to it with an assembly gap (AG) and discordant 10X linked reads in this region. In contrast, the trio-based assembly (bTaeGut2.pat.W) had no NPNT-like gene, suggesting a false gene gain in bTaeGut1.0. The false duplication we found in this region was collapsed by purge_dups, and the falsely segmented gene structure was recovered. The VGP assembly v1.7 pipeline with purge_dups conducted before scaffolding prevented this false duplication (Additional file 2: Fig. S12). b Dot plot of alignment showing large ~1.9 Mbp false duplication of chromosome 29 (apricot) in the zebra finch VGP v1.0 pipeline assembly, bTaeGut1.0. c The large ~1.9 Mbp of duplications of chromosome 29 in bTaeGut1.0 were prevented in the trio-based assembly. d The 1.8 Mbp duplication was prevented with purging pre-scaffolding in bTaeGut1.4 using the VGP v1.7 pipeline. The boundaries of the scaffolds are represented as gray dashed lines

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