domains / families / science / genome-assembly-pipeline

genome-assembly-pipeline

separate

Orchestrates an end-to-end de novo genome assembly project, routing each step to the right genome-assembly skill rather than restating it. Profiles the genome first (k-mer spectrum -> size, heterozygosity, ploidy), QCs reads, chooses an assembly path by data type (SPAdes for Illumina, Flye for noisy long reads, hifiasm for HiFi, metaFlye for communities), polishes only when needed, decontaminates, scaffolds with Hi-C, and finishes with three-axis QC (contiguity + completeness + correctness). Use when assembling a genome from raw reads and deciding which assembler, whether to polish, and how to prove the result is good.

When to use

• assembling a genome from raw reads
• deciding which assembler to use
• determining whether to polish
• proving the result is good
• profiling genome size and heterozygosity
• QCing reads
• decontaminating assemblies
• scaffolding with Hi-C

When not to use

• restating individual genome-assembly skills
• providing full option sets for specific tools

Skill page

Source