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.

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 R 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."

• AssemblerFlow
• Nextflow
• RStudio

Data

Unicycler sample data

Pre-requisites

Some familiarity with genome assembly. No need for prior knowledge in AssemblerFlow or NextFlow: they can be learned during the hackathon.