SRPRISM - Single Read Paired Read Indel Substitution Minimizer

Version 3.3.3-pre

For questions regarding SRPRISM, please contact Aleksandr Morgulis (morgulis@ncbi.nlm.nih.gov) or Richa Agarwala (agarwala@ncbi.nlm.nih.gov)

Linux Compilation

Download current source code for SRPRISM
$ git clone https://github.com/ncbi/SRPRISM

Do following:
$ cd SRPRISM/srprism

To enable support for NGS library, needed to access NCBI SRA archive directly,
please uncomment the following line in the beginning of the top level Makefile
# export USE_SRA = 1
This will trigger automatic download and compilation of the NGS library.
In order to use pre-installed NGS and VDB libraries, uncomment the following
lines in the top level Makefile and change them to point to the relevant paths
# export NGS_PATH =
# export VDB_PATH =

To build SRPRISM application, do
$ make

After successful build, srprism executable can be found in app/ subdirectory.

Windows Compilation

Windows 64-bit version of SRPRISM was tested with MS Visual Studio 2022 and
MS Visual Studio 2022 Community Edition. In order to compile the following
is required:

    - MS Visual Studio 2022 (or Community Edition of it);
    - if cloning from github: git with git bash (available here: https://git-scm.com/download/win)

To compile:

    - select a work directory (in the following $SRP_HOME is used as a
        full pathname of that directory);
    - to clone the latest version: start git bash and issue the following commands:
        cd $SRP_HOME
        git clone https://github.com/ncbi/SRPRISM
    - to use the latest stable release: download the latest .zip archive from
      github.com/ncbi/SRPRISM/releases and unpack it in $SRP_HOME
    - start MS Visual Studio 2022 and open solution: $SRP_HOME\SRPRISM\windows\SRPRISM\SRPRISM.sln
    - select Release/x64 configuration
    - in the "Solution Explorer" pane, right click on the solution and select "build solution" in
      the context menu
    - the final executable SRPRISM.exe will be in $SRP_HOME\SRPRISM\windows\SRPRISM\x64\Release\

Usage

Please see srprism/README file for usage infromation and examples.