centroFlye: Assembling Centromeres with Long Error-Prone Reads
Creators: name: Bzikadze, Andrey
name: Pevzner, Pavel A.
Publisher: name: Zenodo
Year: 2019
Subjects: genome-assembly
centromere
genomics
long-reads
long-read-sequencing

description: Assembly for cenX (v0.8.3) can be found at <strong>centroFlye_results/polishing/final_sequence_4.fasta</strong>. Assembly for cen6 (v0.1.3) can be found at <strong>centroFlyeMono_results_cen6/centroFlyeMono_cen6/polishing/scaffold_0/scaffold_0.fasta</strong> Description of directories.<br> Steps of centroFlye pipeline are synced to `README.md` (`Pipeline`) of centroFlye main [github](https://github.com/seryrzu/centroFlye). <strong>abnormal_12_mers</strong> --- dot-plots of 12-alpha-mers of putative abnormal structure (not like DXZ1*). Most of them are actually fine. See <strong>Appendix: Abnormal units in centroFlye cenX assembly</strong> <strong>abnormal_units</strong> --- dot-plots of units with not 12-alpha-mer structure. See <strong>Appendix: Abnormal units in centroFlye cenX assembly</strong> <strong>cen6_hor_graph</strong> — de Bruijn graphs for detecting HOR structures in cen6. See <strong>Appendix: Assembly of centromere on chromosome 6</strong> <strong>centroFlye_results</strong> --- results of centroFlye for centromere X of CHM13 cell line. See main part of the paper and <strong>README.md</strong> at centroFlye main github <strong>centromeric_reads</strong> --- directory containing centromeric reads. See <strong>Methods: Recruiting centromeric reads, Figure 2.1</strong> and <strong>1. Recruitment of centromeric reads</strong> step of centroFlye pipeline <strong>DXZ1_star</strong> --- contains DXZ1* (and its homopolymer-compressed version). See <strong>Appendix: Deriving accurate consensus HORs</strong> and <strong>5. Obtaining a polished version of DXZ1 (DXZ1* in the paper) supported by centromeric reads</strong> step of centroFlye pipeline <strong>NCRF_rc</strong> --- NCRF report on centromeric reads on DXZ1. See <strong>Methods: Partitioning centromeric reads into units (Figure 2.2)</strong> and <strong>2. Partitioning centromeric reads into units, where each unit represents a HOR copy</strong> step of centroFlye pipeline <strong>polishing</strong> --- polished version of assembly (the assembly itself is <strong>final_sequence_4.fasta</strong>). See <strong>Methods: Reconstructing the centromere (Figure 2.6)</strong> and <strong>6. Polishing</strong> step of centroFlye pipeline <strong>recruited_unique_kmers</strong> --- recruited k-mers used as stepping stones of assembly. See <strong>Methods: Identifying rare centromeric k-mers (Figure 2.4)</strong> and <strong>Methods: Constructing the distance graph (Figure 2.5)</strong>. See <strong>3. Recruitment of unique k-mers</strong> step of centroFlye pipeline <strong>tr_resolution</strong> --- placement of reads by units in the cenX. See <strong>Methods: Reconstructing the centromere (Figure 2.6)</strong> and <strong>4. DXZ1 array resolution</strong> step of centroFlye pipeline <strong>centroFlyeMono_results_cen6</strong> --- results of centroFlye<sub>mono</sub> for centromere 6 of CHM13 cell line. See <strong>Appendix: Assembly of centromere on chromosome 6 </strong>and <strong>README.md</strong> at centroFlye main github <strong>D6Z1</strong> — version of D6Z1 and its monomers used in the study (genbank <strong>AB005791.1</strong>) <strong>DXZ1</strong> --- version of DXZ1 used in the study (genbank <strong>X02418.1</strong>, reversed-complement) <strong>DXZ1_gorilla</strong> --- version of DXZ1 from gorilla used in <strong>Appendix: Variations in HORs provide insights into evolutionary history of cenX</strong> <strong>LINE</strong> --- LINE element that was found in cenX (genbank <strong>GU477636.1</strong>) <strong>nanosim_training</strong> --- results of [Nanosim](https://github.com/bcgsc/NanoSim) training on T2T CHM13 cell line (first 1m reads). See <strong>Appendix: Benchmarking centroFlye on simulated datasets</strong> <strong>rel2</strong> --- necessary files from release 2 of T2T CHM13 (available at [github](https://github.com/nanopore-wgs-consortium/CHM13)). See <strong>Appendix: Analyzing non-uniform read coverage of the T2T4 read-set</strong> <strong>rel3</strong> --- necessary files from release 3 of T2T CHM13 (available at [github](https://github.com/nanopore-wgs-consortium/CHM13)) <strong>simulations</strong> --- results of simulations and centroFlye performance on them. See <strong>Appendix D. Benchmarking centroFlye on simulated datasets</strong> <strong>subsampling</strong> — centroFlye performance on subsampled data. See <strong>Appendix N: Effects of downsampling and read trimming on centromere assembly </strong> <strong>T2T</strong> --- directories with T2T assemblies and NCRF results on them (using DXZ1*). See <strong>Results: centroFlye and Telomere-to-Telomere assemblies of cenX</strong>