Algorithm Architecture & Decision Matrices
Detailed comparison cards highlighting algorithmic trade-offs, strengths, weaknesses, and recommended production setups.
Primary Software & Algorithms in Genome Assembly & Pangenomics
Direct command-line recipes, Conda environment specifications, memory footprints, and license metadata.
Haplotype-resolved de novo genome assembler designed for PacBio HiFi reads. Produces fully phased maternal and paternal haplotype assemblies with ultra-low error rates.
conda install -c bioconda hifiasm
Fast and robust de novo assembler for single-molecule long reads (ONT and PacBio). Builds repeat graphs from error-prone reads without preliminary error correction.
conda install -c bioconda flye
Versatile de novo assembler for bacterial, fungal, viral, single-cell MDA, and metagenomic short reads using iterative multi-sized de Bruijn graphs.
conda install -c bioconda spades
Ultra-fast, ultra-low memory de novo assembler for large-scale metagenomic data (soil, ocean, gut). Capable of assembling terabytes of sequencing reads on a single server.
conda install -c bioconda megahit
Nanopore de novo long-read assembler designed to produce a human genome assembly in hours using marker k-mers and Linux shared memory POSIX primitives.
conda install -c bioconda shasta
Tool for reference-guided scaffolding, assembly improvement, and structural variant discovery. Orders and orients draft contigs against high-quality reference genomes.
conda install -c bioconda ragtag
Bioinformatics Application for Navigating De novo Assembly Graphs Easily. Visualizes GFA/FASTG contig connection paths, repeat bridges, and blast hits interactively.
conda install -c bioconda bandage
Proceed to Stage 9: Metagenomics, Microbiome & Functional Pathways
Sequencing pipelines proceed sequentially. Move forward to the next analytical domain to explore downstream algorithms and execution profiles.