Documentation for Snakemake workflow "genome hybrid assembly"

This workflow creates state-of-the-art genome hybrid assemblies for diploid vertebrate species. This version of the workflow was developed for the following scenario:

• input species: human
  • successfully tested as well: muntjac
• assembler: Verkko v1.4.1
  • hifiasm v0.19.x is not yet fully integrated
• inputs:
  • long accurate reads: PacBio HiFi (Sequel-II/Revio)
    • required coverage: at least ~40X, ideally ~60X
  • long connecting reads: Oxford Nanopore ultralong (R9)
    • required coverage: ~30X ultralong (>100 kbp) reads
  • optional input for phasing:
    • trio: kmer databases created with meryl
    • HiC: HiC short reads
    • graph/node coloring for Verkko's Rukki (GFA file)
• outputs:
  • main: whole-genome assembly, potentially phased
  • main: basic (length) statistics about assembly and long reads
  • optional: a coordinate map between the homopolymer-compressed assembly graph and the linearized plain FASTA files

If you are familiar with the templated Snakemake workflow interface of the CUBI, please proceed directly to the specific instructions for configuring this workflow.

Otherwise, please also read the short user documentation in the next section to learn how to setup and run the workflow and what file accounting is. The process of file accounting is used to generate a manifest file for the workflow run that tracks all input, output and reference files, if applicable.

User documentation for workflow template

All standard workflows of the CUBI implement the same user interface (or at least aim for a highly similar interface). Hence, before executing the workflow, we strongly recommend reading through the documentation that explains how we help you to keep track of your analysis results; we refer to this concept as "file accounting". This feature of standard CUBI workflows enables the pipeline to auto- matically create a so-called "manifest" file for your analysis run.

In case of questions, please open a GitHub issue in the repository of the workflow you are trying to execute.

Developer documentation

Besides reading the user documentation, CUBI developers find more information regarding standadized workflow development in the developer notes. Please keep in mind to always cross-link that information with the guidelines published in the CUBI knowledge base.

Please raise any issues with these guidelines "close to the code", i.e., either open an issue in the knowledge base repo or in the affected repo for more specific cases.