gcsa-locate

This tool uses GCSA2 index to locate k-mers in the underlying graph.

Installation

Installing dependencies

• g++ (>= 4.9)

• zlib (>=1.2.8) and bz2 libraries:

  sudo apt-get install zlib1g-dev libbz2-dev
  

• Seqan2 (>=2.3.2): you can download seqan package from here. Then, unpack the library package to PREFIX (e.g. /usr/local). Make sure that the seqan-2.pc located in the $PREFIX/lib/pkgconfig directory contains correct value for prefix; e.g. in case that the library is installed in /usr/local, it should be:

  prefix=/usr/local
  

• SDSL library (>=2.1.0): to download and install SDSL library see its GitHub page.

• GCSA2 (>=1.0.0): this library does not provide a proper installation script. After compiling the library, you can use this script to install the library to PREFIX (e.g. /usr/local):

  chmod u+x install.sh
  ./install.sh /usr/local
  

Building gcsa-locate

In order to build the tool, simply run:

./autogen.sh  # if it is compiled from a git clone.
./configure
make
sudo make install

Usage

Consult with the man page:

man gcsa_locate