Additional file 1 of Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres
Creators: name: Tan, Kar-Tong
name: Slevin, Michael K.
name: Meyerson, Matthew
name: Li, Heng
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Additional screenshots of basecalling repeat errors found on different chromosomal arms. Figure S2. Examples of long-reads with three types of basecalling error repeats found at telomeres. Figure S3. Co-occurrence heatmap illustrating the frequency of co-occurrence of telomeric repeats and basecalling errors for the CHM13 nanopore dataset generated at different sites. Figure S4. Frequency of telomeric repeats and repeat artefacts on each chromosomal arm. Figure S5. Mapping error rate of long-reads simulated from terminal ends of the CHM13 reference genome. Figure S6. Negligible bias in read coverage of each of the chromosomal arms was observed in the nanopore sequencing dataset for the CHM13 sample. Figure S7. Frequency of telomeric repeat errors in different nanopore sequencing dataset and sequencing platforms. Figure S8. Frequency of telomeric repeat errors in different nanopore basecallers. Figure S9. Co-occurrence heatmap for different nanopore basecalling models. Figure S10. Frequency of telomeric repeats and repeat artefacts on each long read. Figure S11. Current profiles for telomeric repeats in reads of low read qualities, or in reads of high read qualities. Figure S12. Similarities between current profiles for all possible pairs of 6-mer repeats. Figure S13. Example of reads with (GT)n repeat sequences in the CHM13 dataset. Figure S14. IGV screenshots depicting repeat calling errors observed on telomere-like repeat sequences in the CHM13 dataset. Figure S15. Simulated current profiles for 10 consecutive repeats of the telomere-like repeat sequences, and observed repeat calling errors. Figure S16. Repeats with predicted similarity in current profiles to the three types of telomere-like repeat sequences. Figure S17. Frequency of natural telomeric repeats, and repeat calling errors in nanopore datasets for each organism assessed. Figure S18. Repeat calling errors are present on the telomeres of Chicken which are characterized by (TTAGGG)n repeat sequences. Figure S19. Repeat calling errors are present on the telomeres of Arabidopsis thaliana which are characterized by (TTTAGGG)n repeat sequences. Figure S20. Repeat calling errors are present on the telomeres of some Caenorhabditis elegans nanopore datasets. C. elegans telomeres are characterized by (TTAGGC)n repeat sequences. Figure S21. Repeat calling errors are absent on the telomeres of Saccharomyces cerevisiae which are characterized by (TG1–3)n repeat sequences. Figure S22. No differences in basecalling was observed between different strands at the terminal end of Drosophila melanogaster. Figure S23. Additional examples for the performance of the tuned bonito basecaller on telomeres on other chromosomal arms. Figure S24. Histograms depicting the frequencies of 3-mer repeats on reads at telomeres and on reads found at the rest of the genome in the CHM13 dataset.