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assembly-qc

separate

Evaluates genome assembly quality across the three orthogonal axes - contiguity (QUAST auN/NG50/NGx, not bare N50), completeness (BUSCO/compleasm gene-space plus Merqury k-mer completeness), and correctness (reference-free Merqury QV, Inspector/CRAQ structural errors, asmgene false-duplication/collapse). Covers why N50 is the most-gamed metric, why QV measured on the polishing reads is circular, distinguishing uncollapsed haplotigs from real WGD, and the EBP/VGP 6.C.Q40 standard. Use when judging whether an assembly is good enough to annotate or publish, comparing assemblers, diagnosing a fragmented or duplicated assembly, or assessing a phased diploid assembly.

When to use

• judging whether an assembly is good enough to annotate or publish
• comparing assemblers
• diagnosing a fragmented or duplicated assembly
• assessing a phased diploid assembly
• measuring contiguity, completeness, and correctness

When not to use

• using bare N50 as the sole quality metric
• computing QV on polishing reads
• using QUAST structure metrics against a divergent relative

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