Additional file 1 of NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads
Creators: name: Khelik, Ksenia
name: Sandve, Geir
name: Nederbragt, Alexander
name: Rognes, Torbjørn
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Genetics
subject: Evolutionary Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 1: Supplementary materials. Figure S1. NucBreak workflow. Figure S2. Properly mapped read pair formation. The black line represents an assembly. The arrows represent all possible read mapping locations. The cases a) and b) correspond to the situations when no read pairs are formed or just one read pair is formed, respectively. The cases c) and d) show examples when several read pairs are formed from two given reads. The case d) is an example of the situation when reads are mapped to a tandem repeat. Figure S3. Properly mapped read pair categorization. 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. The arrows represent all possible read mapping locations. Figure S4. Read paths and path gaps. 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. The arrows of the same colour correspond to the read paths of the same type. The rectangles between the read paths indicate path gaps. The example demonstrates the correct order of the read paths in the absence of assembly errors. Figure S5. Possible type order and locations of read paths in the absence of breakpoints. Figure S6. Sensitivity results for the insertion, duplication and tandem duplication groups, obtained using the simulated datasets. Figure S7. Sensitivity results for the deletion, deletion_repeat and deletion_tandem groups, obtained using the simulated datasets. The deletion_repeat group contains deletions of interspersed repeats or their parts. The deletion_tandem group contains deletions of tandem repeats or their parts. Figure S8. Sensitivity results for the inversion, relocation and relocation_overlap groups, obtained using the simulated datasets. The relocation group consists of relocations with either inserted regions between misjoined regions (size varied between 10 and 1000) or without them (size is equal to 0). The relocation_overlap group consists of relocations with overlapped misjoined regions. Figure S9. Sensitivity results for the insertion, duplication and tandem duplication groups, obtained using the simulated datasets. Figure S10. Sensitivity results for the deletion, deletion_repeat and deletion_tandem groups, obtained using the simulated datasets. The deletion_repeat group contains deletions of interspersed repeats or their parts. The deletion_tandem group contains deletions of tandem repeats or their parts. Figure S11. Sensitivity results for the inversion, relocation and relocation_overlap groups, obtained using the simulated datasets. The relocation group consists of relocations with either inserted regions between misjoined regions (size varied between 10 and 1000) or without them (size is equal to 0). The relocation_overlap group consists of relocations with overlapped misjoined regions. Figure S12. Sensitivity results for the insertion, duplication and tandem duplication groups, obtained using the datasets from the Assemblathon 1 project. Figure S13. Sensitivity results for the deletion, deletion_repeat and deletion_tandem groups, obtained using the datasets from the Assemblathon 1 project. The deletion_repeat group contains deletions of interspersed repeats or their parts. The deletion_tandem group contains deletions of tandem repeats or their parts. Figure S14. Sensitivity results for the inversion, rearrangement and rearrangement_overlap groups, obtained using the datasets from the Assemblathon 1 project. The rearrangement group consists of relocations and translocations with either inserted regions between misjoined regions (size varied between 1 and 1000) or without them (size is equal to 0). The rearrangement_overlap group consists of relocations and translocations with overlapped misjoined regions. Figure S15. Sensitivity results for the reshuffling and substitution groups, obtained using the datasets from the Assemblathon 1 project. Figure S16. Sensitivity results for the insertion, duplication and tandem duplication groups obtained using the bacterial genome datasets. Figure S17. Sensitivity results for the deletion, deletion_repeat and deletion_tandem groups, obtained using the bacterial genome datasets. The deletion_repeat group contains deletions of interspersed repeats or their parts. The deletion_tandem group contains deletions of tandem repeats or their parts. Figure S18. Sensitivity results for the inversion, rearrangement and rearrangement_overlap groups, obtained using the bacterial genome datasets. The rearrangement group consists of relocations and translocations with either inserted regions between misjoined regions (size varied between 1 and 1000) or without them (size is equal to 0). The rearrangement_overlap group consists of relocations and translocations with overlapped misjoined regions. Figure S19. Sensitivity results for the reshuffling and substitution groups, obtained using the bacterial genome datasets. Table S1. Genome modifications implemented during the simulation process. G and A denote a reference genome and assembly, respectively. All other letters denote reference genome and assembly sequence regions. Diff means difference. C′ is the reverse complement of C. Table S2. List of bacterial genomes. Table S3. Number of ground truth errors in each group.