Algorithm Architecture & Decision Matrices
Detailed comparison cards highlighting algorithmic trade-offs, strengths, weaknesses, and recommended production setups.
Primary Software & Algorithms in Epigenomics & Chromatin Regulation
Direct command-line recipes, Conda environment specifications, memory footprints, and license metadata.
Model-based Analysis of ChIP-Seq and ATAC-Seq data. Dynamically estimates local Poisson backgrounds to call narrow transcription factor binding sites and broad histone marks.
conda install -c bioconda macs3
User-friendly suite for deep-sequencing data exploration. Generates normalized BigWig coverage files (RPGC/1x, RPKM), computes matrix heatmaps across TSS regions, and QC fingerprint plots.
conda install -c bioconda deeptools
Maps bisulfite-treated sequencing reads (WGBS, RRBS) to reference genomes and determines cytosine methylation context (CpG, CHG, CHH) with base-resolution methylation call extractors.
conda install -c bioconda bismark
Integrates multi-histone mark ChIP-seq data to learn de novo chromatin states (active promoters, strong enhancers, Polycomb repression, heterochromatin) via Hidden Markov Models.
conda install -c bioconda chromhmm
Blazing-fast methylation extractor for bisulfite sequencing BAM files. Generates per-base CpG, CHG, and CHH methylation percentage bedGraph and bigWig files in minutes.
conda install -c bioconda methyldackel
Standard package for storing, querying, and manipulating 2D genomic contact matrices (Hi-C, Micro-C, GAM). Efficient multi-resolution zoomify trees for high-res chromatin folding maps.
pip install cooler
Proceed to Stage 8: Genome Assembly, Scaffolding & Pangenomes
Sequencing pipelines proceed sequentially. Move forward to the next analytical domain to explore downstream algorithms and execution profiles.