sanger-tol / sequencecomposition Goto Github PK

https://github.com/piosierra/pantera

https://www.biorxiv.org/content/10.1101/2024.04.05.588311v1.full.pdf

Description of feature

Update to the latest nf-core pipeline template

Description of feature

Implement nf-validation for parameters and sample sheets

Description of feature

Import features from GDA (Genome Decomposition Analysis) pipeline

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

Description of feature

Data could then be browsed on UCSC/Ensembl

Which pipeline(s) is your feature request for?

• insdcdownload
• ensemblrepeatdownload
• ensemblgenedownload
• sequencecomposition
• readmapping
• variantcalling
• blobtoolkit
• genomenote

Describe the solution you'd like.

Import features from GDA (Genome Decomposition Analysis) pipeline

Is your feature request related to a problem? Please describe.

No response

Describe alternatives you've considered.

No response

Additional context.

No response

Code of Conduct

• I agree to follow this project's Code of Conduct

Description of feature

And a "cleanup" profile

Description of feature

Add TRASH (Tandem Repeat Annotation and Structural Hierarchy) pipeline