Hackseq 2018

Hackseq 2018: Mix and match modular genome assembler components

Genome sequencing yields many short reads of DNA from a genome. Genome assembly attempts to reconstruct the original genome from these reads. Most genome assembler software tools are pipelines of many stages. It's not however typical to mix and match stages from different tools. Our Hackseq project aims to create a better assembly tool by mixing and matching components of various assembly tools.

We will work together to create modular assembler components for AssemblerFlow, a tool which builds pipelines of tools for genome assembly using Nextflow. Each participant will create and run a genome assembly pipeline using AssemblerFlow. We will assess the quality of each assembly, using Quast. Finally, we'll create a leader board of awesomeness to compare the assembly results!

Plan

Create assembler components for AssemblerFlow.

• ABySS
• BCALM
• SPAdes
• Unicycler

Bake off!

• Each participant will create and run an AssemblerFlow pipeline
• Assess the quality of each assembly (using Quast)
• Create a leader board of awesomeness! (using RStudio's Shiny or Flexdashboard)

Tools

AssemblerFlow builds pipelines of tools for genome assembly. "A Nextflow pipeline assembler for genomics. Pick your modules. Assemble them. Run the pipeline."

Data

Unicycler sample data

Prerequisites

• familiarity with the command line and shell scripts is needed
• familiarity with a scripting language such as Python or R is useful
• some familiarity with genome assembly is helpful, but not required
• no need for prior knowledge in AssemblerFlow or NextFlow: they can be learned during the hackathon