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Read-only view of a live SciFlow workflow — this is the actual pipeline that produced these results, not a mockup. Long-Read Genome Assembly — HiFi (HG002) + Nanopore (E. coli). Open any stage to inspect its parameters, command, versions, inputs and outputs.
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Apr 28, 2026
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Created Apr 29, 2026 at 04:14
Assemble genomes from long reads — both human-scale PacBio HiFi and bacterial-scale Oxford Nanopore — and benchmark the result properly. Drop in HiFi reads (HG002 chr20 in this demo) or ONT R10.4.1 reads (E. coli K-12 here), and the pipeline returns a contig-level assembly, a polished consensus where appropriate, and the QC numbers that actually tell you whether to trust it. Built for reference-grade assembly projects, T2T-style finishing efforts, microbial completion work, and anyone tired of getting a FASTA with no error estimate attached to it. Which platform, what was your QV, how complete is the gene set — those are the questions, and the pipeline answers all three. HiFi data goes through hifiasm in its primary configuration. ONT data runs through Flye (--nano-hq) and is then polished by Racon over two rounds, re-aligning the raw reads to refine the consensus. Merqury delivers a reference-free quality value (QV) from k-mer concordance with the reads, and compleasm reports gene-level completeness using miniprot — faster and more honest on long-read assemblies than the older BUSCO pipeline. The output is a contigs FASTA, an assembly graph, a QV number you can quote, and a completeness percentage with the lineage labeled.