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Scaffolding with ScaRa

This repository contains OLD python scripts and binaries comprising our ScaRa tools for genome scaffolding.

ScaRa is based on Ezra scaffolding tool (http://complex.zesoi.fer.hr/data/pdf/Ivan_Krpelnik_diplomski.pdf) and uses come concepts from the HERA scaffolder paper (https://www.biorxiv.org/content/early/2018/06/13/345983). It consists of two phases, extension phase and bridging phase, each can be run multiple time. Extension phase uses MSA (Multiple Sequence Alignment) and POA (Partial OrderAlignment) graphs, while bridging phase constructs paths betwewen contigs using reads that overlap and then tries to determine the best path.

ScaRa uses Minimap2 to generate everlaps as needed, and can use Racon to correct the contigs at the start, et the end od after each iteration of the scaffolding process.

Installation

  1. Clone the repository, and include all submodules.
git clone --recursive https://github.com/kkrizanovic/ScaRa.git

Note: if you omitted <--recursive> from <git clone>, run <git submodule update --init --recursive> before proceeding.

  1. Build Ezra
cd Ezra
mkdir build
cd build
cmake ..
make
  1. Build Minimap2
cd Minimap2
make
  1. Build Racon
cd racon
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make

Pythons scripts, such as Bridger, ScaRa and Samscripts tool do not need to be installed.

Dependencies

Python scripts require PYthon2.7. Ezra and Racon require CMake 3.5.

Running ScaRa

ScaRa is run using <scara.py> script from the root folder of the repository.

A basic command for running ScaRa:

python scara.py contigs.fasta reads.fastq --results results_folder

Available options will be printed out when running the script without arguments.

The scaffolding will run in several iterations for more complete and correct scaffolding. The script will generate a separate folder for each iteration of scffolding. The final result will be in the root results folder named <scara_scaffolds_final.fasta>.

Racon ScaRa script can also be instructed run Racon on the initial contigs, on the final scaffolds and after each iteration of scaffolding. This can be specified using options:

  • <--racon-start> - run racon on the initial contigs, before scaffolding
  • <--racon-end> - run racon on the final scaffold
  • <--racon> - run racon after each iteration

Minimap2 ScaRa will run Minimap2 to calcualte overlaps as needed for the scaffolding and also for Racon.