Long-Read Assembly QC and Tools

Predict how Oxford Nanopore read length and error patterns and Illumina read accuracy affect isolate assembly, polishing, and quality-control decisions.

Construct a NanoPlot command for Oxford Nanopore FASTQ data and explain the purpose of its principal input and output options.

Interpret NanoPlot yield, read-length, N50, quality-score, and length-versus-quality outputs to judge whether a long-read dataset is suitable for bacterial isolate assembly.

Construct minimap2 commands for Oxford Nanopore read-to-assembly and assembly-to-reference alignment, choosing appropriate presets and PAF or SAM output.

Interpret minimap2 alignment and coverage evidence to identify unsupported assembly regions, structural discrepancies, and possible contamination.

Select between a Unicycler hybrid assembly and an Autocycler ensemble long-read assembly based on the available reads and the intended result.

Construct a Unicycler command for paired Illumina reads plus Oxford Nanopore reads, then interpret its log, assembly graph, contigs, and circularization status.

Trace Autocycler's staged consensus workflow, construct its principal commands, and interpret its clustering and resolved consensus outputs.

Construct a Polypolish workflow using paired Illumina alignments and explain how multi-mapping evidence supports conservative correction of a long-read assembly.

Run QUAST and interpret assembly size, contig count, N50, GC content, reference-based discrepancies, and warnings in the context of a bacterial isolate.

Run CheckM and interpret lineage placement, completeness, contamination, and strain-heterogeneity estimates when deciding whether an assembly is fit for downstream use.