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!

Abstract

Background

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. These tools all work towards the same goal using different methods, and new tools allow for interoperability between all the different stages of different assemblers.

Problem

It is not common to mix and match stages from all the different assembly tools into one and understand the benefits or the disadvantages of doing that, specifically towards understanding the improvement of the assembly quality. Therefore our Hackseq project aims to create a better assembly tool by mixing and matching components of various assembly tools, and visualising the results of this work. The assembly tools that we are considering are displayed here.

Solution

We have attempted to solve this problem by creating modular assembler components for AssemblerFlow, a tool which builds pipelines of tools for genome assembly using Nextflow, and we have created components for a number of assembly tools.

Plan

1. Create assembly components
   Package up existing assembly tools
2. Develop the pipeline glue that sticks components together
   using Flowcraft, Nextflow, Snakemake, GNU Make, or shell
3. Compose an assembly pipeline of specific tools
   for example, Bcalm → ABySS bubble popping → ABySS repeat resolution → …
4. Assess assembly correctness and contiguity
   Display a constantly-updating leader board of awesomeness

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)
• For inspiration, see http://nucleotid.es/benchmarks/

Tools

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

Software installation instructions

Install Homebrew on macOS and Linuxbrew on Linux and Windows 10, using Windows Subsystem for Linux (WSL).

macOS

Install XCode.

xcode-select --install
brew cask install bandage docker igv java r-app rstudio
open -a Docker

Windows

Install Windows Subsystem for Linux (WSL).

Linux and Windows

Install RStudio.

brew install jdk@8 r linuxbrew/extra/singularity brewsci/bio/bandage

All operating systems

brew tap brewsci/bio
brew install abyss bcalm bwa flowcraft igv miniasm minimap2 ntcard pilon samtools spades unicycler

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