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描述
Description of feature
stainedglass is particularly useful for disentangling tandem repeat structures and segmental duplications. Under the hood, it is a snakemake workflow of bwa mem alignments of chunked genome + some custom scripts for transformation of the alignments into a heatmap. It can produce higlass-compatible cooler output:
cd StainedGlass
samtools faidx ref.fa
snakemake --use-conda --cores 16 cooler_density --config nbatch=4 alnthreads=4 fasta=ref.fa window=32 cooler_window=100 sample=sample_id