README for T2T-chm13v2 HSat123 analyses

for Altemose N, 2022, Seminars in Cell and Developmental Biology, https://doi.org/10.1016/j.semcdb.2022.04.012

open-access preprint: https://www.preprints.org/manuscript/202202.0009/v2

Input Tables and Sequences

1) CHM13v2.0_HSat123_Strand_Subfam_DistinctArrays.bed

[copied into main directory, here] This contains information on all HSat1-3 arrays in the chm13v2.0 assembly.

Columns are chr, start, end, family/subfamily, 0, strand, start, end, rgb color, array index (chr_family_number; "small" if <10 kb), number of inversion breakpoints

2) chm13v2.0_hsat*_DistinctArrays_FWD.fasta.gz

This was produced by obtaining sequences from all distinct arrays >10kb, flipping them to the FWD orientation, and concatenating discontiguous subarrays with 50k Ns sandwiched between. These are the output of Merge_HSat123_Fastas.pl

Output Files

1) Shared_24mer_matrices contains source data used to generate Fig. 2

Each entry in the matrix represents the proportion of the smaller array

"contained in" the larger array, when broken into 24-mers

Entries along the diagonal represent the 24-mer fold compression of the array,

i.e. the ratio of the array length to the total number of unique 24-mers

these are the output of Count_kmers.pl

2) NTRprism_output

The tophits files produced by NTRprism_ProcessFasta_v0.3e.pl with default parameters and a max span of 20000

Columns are array index, top repeat unit lengths, column sum values for each length (same order), the best 6-mer for yielding fragments of each length (same order), the proportion of the array covered by fragments of each length when digested by its best kmer (same order)

3) Consensus_sequences

HSat123_consensus_sequences.fa contains simple consensus sequences derived from multiple alignments in Multiple_Alignments. Commands for producing these sequences and for executing other code are present in Command_Execution.sh