HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data

GENA-LM is a transformer masked language model trained on human DNA sequence.

a Semi-automated pipeline for assembling T2T genome

tensor2tensor usage

Centromere calculation from TRASH-derived repeat arrays: block merging, filtering, and gap profiling.

Mapping And Prediction of Shared Elements in Alignments

Pipeline for telomere-to-telomere QC of genome assemblies: assembly stats, telomere detection, gap analysis, clustering, and visualization.

Snakemake workflow to generate BAM alignment statistics on the BIH cluster.

T2T (UCSC hs1) mapping pipeline for human WGS (SRA) using SGE + Singularity. Originally built for schizophrenia neuron TE analysis.