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Read-only view of a live SciFlow workflow — this is the actual pipeline that produced these results, not a mockup. Bacterial Isolate Genomics — E. coli K-12. Open any stage to inspect its parameters, command, versions, inputs and outputs.
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Created Jun 02, 2026 at 15:06
A complete short-read bacterial isolate workflow: take paired-end Illumina reads from a single isolate and come back with a draft genome, its quality grade, a full structural/functional annotation, a gold-standard species call, its sequence type, and an antimicrobial-resistance profile — every stage traceable to the tool and database release that produced it. Built for clinical and public-health microbiologists, GenomeTrakr/PulseNet surveillance labs, and anyone characterising a new isolate. The reference dataset is Escherichia coli K-12 (SRA run SRR1770413, Illumina WGS), a fully characterised lab strain — the right control for a demo because its expected genome size (~4.6 Mb), species, MLST type, and resistance phenotype are all known. The pipeline follows the Torsten Seemann bacterial-genomics canon: Shovill assembly, a unified QUAST + BUSCO quality gate, Prokka annotation, GTDB-Tk r220 taxonomy, PubMLST sequence typing, and AMR screening with ABRicate against the NCBI database. SISTR serovar typing is intentionally omitted — it applies only to Salmonella, and K-12 is E. coli.