e00011027 / MSGseqTK

A Metagenomics Shotgun Sequencing Toolkit for NGS read mapping and cleaning based on a novel incremental and parallel FMD-index algorithm

MSGseqTK introduction

MSGseqTK is a Metagenomics ShotGun Sequencing Toolkit for NGS read mapping and cleaning, based on a novel incremental and parallel FMD-index. The core algorithm is an improved bidirectional FM-index (FMD-index) in which traditionally not-allowed null terminals ('\0') are used as sentinal between genomes/chromosomes so an imcremental, parallel and on-the-fly FMD-index merge algorithm is possible. This new algorithm allows MSGseqTK build, update and merge very large databases at whole metagenomic-scale with reasonable time and space.

The main program 'MSGseqTK' takes single or paired-end NGS FASTA/FASTQ files and map/align them to a pre-built metagenomics database. It includes native supports for multi-threading (w/ OpenMP), .gz or .bz2 compressed inputs (w/ zlib), and direct write into binary BAM (or text SAM) output (w/ HTSLIB).

Implementation

MSGseqTK is written in pure C++11, and built with the GNU Autotools (autoconfig/automake), and can be easily installed under Linux, Windows and Mac OS X.

Download

You can download the latest release from GitHub at: https://github.com/Grice-Lab/MSGseqTK/releases. You can clone or fork and pull the source codes from GitHub at: https://github.com/Grice-Lab/MSGseqTK.

Dependencies

MSGseqTK depends on the popular head-only C++ libraries Boost and Eigen3. They are available and often pre-installed on most Linux distributions, and can be easily installed on Windows and Mac OS X. The HTSLIB C library (from SAMtools) is dependent for directly writing alignment into SAM/BAM files. Many Linux OS have HTSLIB in their software repositories. Try your yum, dnf or apt-get for details. For example, you can install it under CentOS by sudo yum install htslib The ZLIB and Boost-IOSTREAMS libraries are optionally dependent for handling GZIP/GZIP2 compressed files, but are not required and can be disabled.

Installation

1. Prepare configuration file using Linux AutoTools, by running the command

autoreconfig -iv

2. Configure installation, by running the command

./configure

You may consider providing additional options, such as --prefix, --exec-prefix, --with-zlib, --with-boost, --with-htslib, etc.

3. Compile and link, by running the command

make

Look for errors and try to resolve them yourself first (by Google). Contact us only if you are sure it is a bug in our programs.

4. (Optionally) Test, by running the command

make check

It may take a while depending on your processor's speed.

5. Install

make install

You may need root privilege to do it, such as using sudo.

Input & Output

All MSGseqTK's tools use standard formats. For example, FASTQ/FASTQ formats for read files, BAM/SAM formats for alignment files, GTF/GFF3 formats for annotation files and sometimes TSV format for list files. Type the program name with -h|--help or without option for detailed help messages for all its tools.

Documentations

Please check the help and documentations at MSGseqTK's home page

Pre-built databases

You need to build an MSGseqTK database before using it tools for analhying metagenomic data. You can build your own database using msgseqtk-build, or alternatively download the pre-built databases.