Automated assembly of centromeres from ultra-long error-prone reads (repository for paper in Nature Biotech, 2020)
Creators: name: Bzikadze, Andrey V.
name: Pevzner, Pavel A.
Publisher: name: Zenodo
Year: 2019
Subjects: genome-assembly
centromere
genomics
long-reads
long-read-sequencing

description: <strong>UPD May 24, 2021</strong>. The latest version of cenX and cen6 assemblies in CHM13 cell line are available as a part of a complete assembly of a human genome generated by the Telomere-to-Telomere Consortium: (github). The following was last edited on <strong>Aug 21, 2020</strong>. Same information can be found in the README inside the attached archive (centroFlye_data_cenXv0_8_3_cen6v0_1_3_20191224-updatedAndUplodaded_20200616.tgz) <br> <strong>Introduction</strong><br> <br> This data collection is aimed to replicate the results in the centroFlye paper (Bzikadze A.V., Pevzner P.A., Nature Biotechnology, 2020).<br> It contains assemblies of cenX and cen6 (CHM13 cell line) that are analyzed in the paper.<br> The centroFlye version that replicates these assemblies (with instructions) can be found in [github](https://github.com/seryrzu/centroFlye/tree/cF_NatBiotech_paper_Xv0.8.3-6v0.1.3).<br> Note that the branch <strong>cF_NatBiotech_paper_Xv0.8.3-6v0.1.3</strong> is dedicated specifically to replicating assemblies in the paper, while the version of centroFlye in the <strong>master</strong> branch can produce more recent assemblies. This data collection can be used for jupyter notebooks in the [github](https://github.com/seryrzu/centroFlye_paper_scripts).<br> That repository contains instructions on how to use it. <br> <strong>Assemblies</strong><br> <br> <strong>cenX</strong>. Assembly of cenX (version <strong>0.8.3</strong>) that is presented in the paper can be found at `centroFlye_results/polishing1/final_sequence_4.fasta`. If you wish to reproduce the results of the paper, please use this version.<br> The same assembly polished by tandemQUAST (15368941c15681ba9353a97f3542bb3ada149287) can be found at <strong>centroFlye_results/final_assembly.fasta</strong> Please note that this version is not discussed in the paper. <strong>cen6</strong>. Assembly of cen6 (version 0.1.3) that is presented in the paper can be found at <strong>centroFlyeMono_results_cen6/centroFlyeMono_cen6/polishing/scaffold_0/scaffold_0.fasta</strong> <br> <strong>Description of data collection</strong> <strong>abnormal_12_mers</strong> --- dot-plots of 12-alpha-mers with non-canonical structure (not like DXZ1*). See `Supplementary Note 3. Abnormal units in centroFlye cenX assembly` <strong>abnormal_units</strong> --- dot-plots of units with not 12-alpha-mer structure. See `Supplementary Note 3. Abnormal units in centroFlye cenX assembly` <strong>centroFlye_results</strong> --- results of centroFlye for<strong> centromere X</strong> of CHM13 cell line. See main part of the paper and README.md at the centroFlye main github (branch <strong>cF_NatBiotech_paper_Xv0.8.3-6v0.1.3</strong>) <strong>centromeric_reads</strong> --- directory containing centromeric (cenX) reads. See `Methods: Recruiting centromeric reads` (Figure 1.1) <strong>DXZ1_star</strong> --- contains DXZ1* (and its homopolymer-compressed version). See `Supplementary Note 5: Deriving accurate consensus HORs` <strong>NCRF</strong> --- NCRF report on centromeric reads on DXZ1. See `Methods: Partitioning centromeric reads into units` (Figure 1.2) <strong>polishing1</strong> --- polished version of assembly (the assembly itself is `final_sequence_4.fasta`). See `Methods: Polishing the reconstructed centromere sequence` (Figure 1.7) <strong>recruited_unique_kmers</strong> --- recruited k-mers used as stepping stones of assembly. See `Methods: Identifying rare centromeric k-mers` (Figure 2.4) and `Methods: Constructing the distance graph` (Figure 2.5) <strong>tr_resolution</strong> --- placement of reads by units in the cenX. See `Methods: Reconstructing the centromere` (Figure 1.6)` <strong>centroFlyeMono_results_cen6</strong> --- results of centroFlyeMono for<strong> centromere 6</strong> of CHM13 cell line. See `Supplementary Note 6. Assembly of centromere on chromosome 6` in the paper and `README.md` at the centroFlye main github (branch <strong>cF_NatBiotech_paper_Xv0.8.3-6v0.1.3</strong>) <strong>centroFlyeMono_cen6</strong> --- results of the main algorithm. Contains dot plots of iterative de Bruijn graphs and polished assembly sequence <strong>centromeric_reads</strong> --- directory containing centromeric reads (cen6). Same method as for cenX <strong>string_decomposer_report</strong> --- report of String Decomposer on cen6 Reads (Dvorkina et al., Bioinformatics, 2020) (commit 83640e3388be7766837e29384884421955ca3126) <strong>string_decomposition_assembly</strong> --- report of String Decomposer on generated cen6 assembly (same commit) <strong>tandemQUAST_report</strong> --- report of tandemQUAST on generated cen6 assembly and cen6 reads (Mikheenko et al., Bioinformatics, 2020) (commit bcfbfd374279c4f3401caaf6cefcafdb4bc9003d) <strong>D6Z1</strong> --- version of D6Z1 used in the study (genbank <strong>AB005791.1</strong>). Monomers that are extracted with Alpha-CENTAURI 0.2 (Sevim et al., Bioinf, 2016) and specially processed. <strong>DXZ1</strong> --- version of DXZ1 used in the study (genbank X02418.1, reversed-complement) <strong>DXZ1_gorilla</strong> --- version of DXZ1 from gorilla used in `Variations in HORs provide insights into centromere evolution`, `Supplementary Figure 5. HOR recombination <strong>LINE</strong> --- LINE element that was found in cenX (genbank GU477636.1) <strong>nanosim_training</strong> --- results of [Nanosim](https://github.com/bcgsc/NanoSim) (commit 77a4393e18c67adddf60427a617499ac352bc9d8) training on T2T CHM13 cell line (first 1m reads). See `Supplementary Note 1. Benchmarking centroFlye on simulated datasets`. <strong>rel2</strong> --- necessary files from release 2 of T2T CHM13 (available at [github](https://github.com/nanopore-wgs-consortium/CHM13)). See `Supplementary Figure 2. Non-uniform coverage of chrX in HG38 with ultra-long reads (longer than 50 kb) <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 `Supplementary Note 1. Benchmarking centroFlye on simulated datasets` <strong>subsampling</strong> --- results of downsampling and read trimming. See `Supplementary Note 6. Assembly of centromere on chromosome 6`: `Effects of downsampling and read trimming on cen6 assembly.` <strong>T2T</strong> --- directories with T2T assemblies and NCRF results on them (using DXZ1*). See `Results: cenX assembly`