LongStrain for longitudinal metagenomic data

This code was used for the paper "An integrated strain-level analytic pipeline utilizing longitudinal metagenomic data".

Requirements

1. Kraken2 (tested with 2.0.8)
   https://ccb.jhu.edu/software/kraken2/

2. Bowtie2 (tested with 0.16.0.1)
   http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

3. samtools (tested with 1.9)
   http://www.htslib.org/doc/

4. This code was written and tested on python 3.6.5, and requires the following packages:

   • numpy (tested with 1.19.5)
   • pysam (tested with 0.16.0.1)
   • pandas (tested with 1.1.5)

   Note: Kraken2, Bowtie2, and samtools need to be added to the PATH Environment Variable. If you encounter issues, please try to run in an environment with these packages.

Install

1. Install the required software and packages

2. Download all files and deposit them under a directory.

Usage

The detailed introduction can be found in the WIKI: https://github.com/BoyanZhou/LongStrain/wiki

Please contact boyanzhou1992@gmail.com for any questions or bug reporting.