amstools

Collection of high-performance biological sequence tools developed in mixed C (file i/o) and C++ (parallel algorithms) with minimal dependencies (only zlib).

List of Tools

• acgt – Print residue statistics and optionally GC and AT contents.
• ngx – Print the contiguity statistics (e.g. N50, L50).
• sc – Print sequence and residue counts.

Building from Source

amstools is cross-platform (Linux/macOS/Windows). Using CMake you can build and install all the tools by the same commands.

Prerequisites

• CMake version 3.16 or higher
• C++ compiler supporting the C++11 standard (e.g. gcc 4.8)
• zlib – to install zlib under Windows you can use vcpkg

Build and Install

$ git clone https://github.com/arminms/amstools.git
$ cd amstools
$ cmake -S . -B build
$ cmake --build build -j 3 # using 3 concurrent threads
$ cmake --install build

The last command on Linux and macOS needs to be preceded by sudo.