stainedglass self-alignment heatmap

[amakunin]

Description of feature

stainedglass is particularly useful for disentangling tandem repeat structures and segmental duplications. Under the hood, it is a snakemake workflow of bowtie2 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

[muffato]

We should favour ModDotPlot which is a faster implementation, though it doesn't yet have mcool support.

[muffato]

Another issue is that stainedglass uses Conda environments defined with the defaults channel, e.g. https://github.com/mrvollger/StainedGlass/blob/main/workflow/envs/env.yaml.
We will have to first de-Anacondify it and then build an appropriate container.