Autocycler, Polypolish, and Read-Mapping Foundations

Explain how an assembler converts overlapping read information into contigs and why repeats and sequencing errors create ambiguity.

Explain the purpose, inputs, outputs, and main assumptions of Shovill or SPAdes before running a short-read assembly command.

Explain why Autocycler requires multiple mostly complete long-read assemblies before generating them with different assemblers and read subsets.

Explain Autocycler compression, clustering, trimming, resolution, and combination in plain language before running the consensus workflow.

Interpret Autocycler cluster metrics and graphs using a step-by-step checklist for automatic acceptance or manual review.

Explain how Polypolish uses aligned short reads to correct a long-read consensus before running and validating the polishing command.

Explain reference mapping, alignments, mapping quality, CIGAR strings, primary and secondary alignments, depth, breadth, and spanning reads before using minimap2 and samtools.