bio-workflows-genome-assembly-pipeline

Name: bio-workflows-genome-assembly-pipeline
Rating: 5 (1 reviews)
Author: bg-szy

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,

1stars

Updated 15 days ago

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Version Compatibility

Reference examples tested with: GenomeScope2 2.0+, meryl 1.4+, Merqury 1.3+, fastp 0.23+, SPAdes 4.0+, Flye 2.9+, hifiasm 0.25+, metaFlye 2.9+, Racon 1.5+, medaka 2.0+, minimap2 2.26+, FCS-GX 0.5+, CheckM2 1.0+, GUNC 1.0+, YaHS 1.2+, QUAST 5.2+, BUSCO 5.5+, samtools 1.19+. Each owning genome-assembly skill is the source of truth for its tool's pinned version.

Before using code patterns, verify installed versions match. If versions differ: