centroFlye paper scripts

This repository contains scripts to replicate results of the centroFlye paper in Nature Biotechnology, 2020 (see Publications).

centroFlye version

centroFlye repository is included as a submodule (note, the used branch: cF_NatBiotech_paper_Xv0.8.3-6v0.1.3). Thus, please, clone the repo with the following command

git clone --recurse-submodules git@github.com:seryrzu/centroFlye_paper_scripts.git

Necessary data

Please, download necessary data from ZENODO (latest version) and place the archive centroFlye_data_cenXv0_8_3_cen6v0_1_3_20191224-uploaded20200407.tar.gz in the root of the repo. Note that the versions of assemblies that are described in the paper and are used here: cenX - v0.8.3, cen6 - v0.1.3. Updated assemblies may be available in the future — they will be described in the master branch of the centroFlye repository.

Extract the data collection with the following command

tar -xvf centroFlye_data_cenXv0_8_3_cen6v0_1_3_20191224-updatedAndUplodaded_20200616.tgz

All information will be extracted in the data directory.

Jupyter notebooks

The following notebooks (in directory jupyters) replicate the results in the paper. Below we specify the section of the paper for each notebook.

• 01-Results-cenX_assembly-dataset.ipynb replicates Results: cenX assembly, dataset description
• 02-Results_SuppNote2_4.ipynb replicates Results (comparison of T2T and centroFlye assemblies) and Supp. notes: 4: Analysis of centromeric reads that do not map to centroFlye assembly, 2: Hanging index test and Breakpoint test
• 03-Results_CentromereEvolutionInsights.ipynb replicates Results: Variations in HORs provide insights into centromere evolution
• 04-Methods_Recruiting_centromeric_reads.ipynb replicates Methods: Recruiting centromeric reads (Figure 1.1)
• 05-Methods_Partitioning_centromeric_reads_into_units.ipynb replicates Methods: Partitioning centromeric reads into units (Figure 1.2)
• 06-Methods_Classifying_centromeric_reads_into_prefix_internal_and_suffix_reads.ipynb replicates Methods: Classifying centromeric reads (Figure 1.3)
• 07-Methods_Identifying_rare_centromeric_k-mers.ipynb replicates Methods: Identifying rare centromeric k-mers (Figure 1.4)
• 08-Methods_Constructing_the_distance_graph.ipynb replicates Methods: Constructing the distance graph (Figure 1.5)
• 09-Methods_Polishing_the_constructed_centromere_sequence.ipynb replicates Methods: Polishing the reconstructed centromere sequence (Figure 1.7)
• 10-Methods_cen6.ipynb replicates Methods: Assembly of cen6, Recruitment of centromeric reads from cen6, Transforming reads into monoreads, Error correction of monoreads, Constructing iterative de Bruijn graph of monoreads, Assembling monocentromere by scaffolding, Translating monocentromere to the nucleotide alphabet
• 11-SuppNote1_Benchmarking_centroFlye_on_simulated_dataset.ipynb replicates Supplementary Note 1: Benchmarking centroFlye on simulated datasets
• 12-SuppNote3_Abnormal_units_in_centroFlye_cenX_assembly.ipynb replicates Supplementary Note 2: Abnormal units in centroFlye cenX assembly
• 13-SuppNote4_DXZ1BothOrient_Alu_NonunifCov.ipynb replicates parts of Supplementary Note 4. Analysis of centromeric reads that do not map to centroFlye assembly (also see jupyter #2)
• 14-SuppNote5_Deriving_accurate_consensus_HOR.ipynb replicates Supplementary Note 5: Deriving accurate consensus HORs
• 15-SuppNote6-Effects_of_downsampling.ipynb replicates Supplementary Note 6. Assembly of centromere on chromosome 6: Effects of downsampling and read trimming on cen6 assembly
• 16-SuppFigure1-Frequencies_of_the_recruited_19-mers_in_the_centroFlye_cenX_assembly.ipynb replicates Supplementary Figure 1: Frequencies of the recruited 19-mers in the centroFlye cenX assembly

Figures in the paper -> Jupyter notebook number

# Figure	# Jupyter notebook
1	Manual
2	Manual
3a	07
3b	09
3cde	02
3d	02
3e	02
4abcd	02
5	02
6	02
S2.1	02
S2.2	02
S3.1	12
S3.2	12, data/abnormal_units
S3.3	12, data/abnormal_12_mers
S3.4	Manual
S4.1	02
S4.2	Can be reproduced with gepard, data/centroFlye_results/centromeric_reads/centromeric_reads.fasta
S5.1	Can be reproduced with gepard data/DXZ1/DXZ1_rc.fasta
S5.2	14
S6.1	10, data/cen6_hor_graph
S6.2 left	cen6 assembly (main algorithm): left saved* in data/centroFlyeMono_results_cen6/centroFlyeMono_cen6/idb/db_k400.dot. pdf can be generated with dot -Tpdf db_k400.dot -o db_k400.pdf
S6.2 right	Manual from S6.2
S6.3	10, data/centroFlyeMono_results_cen6/tandemQUAST_report/report
S6.4	15
S6.5	15, data/subsampling
SF1	16
SF2	13
SF3,4	03
SF5	03 + Manual

Publications

Bzikadze A.V., Pevzner P.A. centroFlye: Assembling Centromeres with Long Error-Prone Reads, 2020, Nature Biotechnology, in press