SASAR

SASAR is a meta-assembly tool to reconcile different assemblies without a reference guide.

Table of Contents

• Introduction
• Users' Guide
  • Installation
  • Usage
  • Example
• Limitations

Introduction

Installation

• Minimap2 version 2.20

  git clone https://github.com/lh3/minimap2
  cd minimap2 && make
  

• gfatools version 0.5

  git clone https://github.com/lh3/gfatools
  cd gfatools && make
  

• Minigraph version 0.15

  git clone https://github.com/lh3/minigraph
  cd minigraph && make
  

• Python 3

  • biopython
  • pandas
  • pybedtools

  # Install eihter by conda or pip
  conda install -c conda-forge biopython
  conda install -c bioconda pybedtools
  conda install -c anaconda pandas
  

• Silix version 1.2.11

  • A tool for Ultra-fast Sequence Clustering from Similarity Networks
  • Make sure Boost libraries are also installed (for Ubuntu issue the following commands, requires root permissions)

  sudo apt-get install libboost-dev
  sudo apt-get install libboost-program-options-dev

  • Install SiLiX, requires root

   wget ftp://pbil.univ-lyon1.fr/pub/logiciel/silix/silix-1.2.11.tar.gz
   tar zxvf silix-1.2.11.tar.gz
   cd silix-1.2.11
   ./configure
   make
   make check
   sudo make install
  

Usage

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usage: python SASAR.py in_dir

Long read assembly reconciliation

Positional arguments:
  in_dir             input directory containing all assemblies

Settings:
  -t INT             number of CPU threads for whole genome alignment
  -i INT             minimum identity confidence score [95]
  -c INT             minimum coverage confidence score [95]
  -m INT             minium overlap length [50000]
  --repeat_size INT  repeat size [50000]

Output options:
  -o PATH            output directory for SASAR-assembly [./SASAR_output]

Other:
  -h, --help         show this help message and exit
  -v, --version      show program's version number and exit

Dataset

Haploid

• D. melanogaster ISO1 (144Mb |ONT 66x)
• A. thaliana Col-0 (130Mb |ONT 130x)
• O. sativa Nipponbare IRGSP1 (380Mb |ONT 34x)
• O. sativa Nipponbare
• S. pennellii (0.9Gb |ONT 160x)

Diploid

• F. ananassa (0.8Gb |PB HiFi 36x)

Docs

Contact

Copyright © 2020 Panpan Zhang ([email protected])

Any question, concern, or bug report about the program should be posted as an Issue on GitHub. Before posting, please check previous issues (both Open and Closed) to see if your issue has been addressed already. Also, please follow these good GitHub practices.