sanger-tol/sequencecomposition

stainedglass self-alignment heatmap

Open

#14 opened on Nov 28, 2023

View on GitHubContributor guide
 (3 comments) (0 reactions) (0 assignees)Nextflow (3 forks)auto 404
help wanteduser request

Repository metrics

Stars
 (2 stars)
PR merge metrics
 (PR metrics pending)

Description

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

Contributor guide

Research direction
Review the repository's Nextflow workflow structure, examine existing processes to understand how to add a new one, and study StainedGlass to see how to incorporate its self alignment heatmap generation into the pipeline. Also read the issue comments for any nuanced requirements.
Tech stack
groovyshell
Domain
databackend
Issue type
Feature
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
3
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
1-2 days
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Mostly clear
Prerequisites
GitNextflowGroovyShell
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
45