StrainKmer

StrainKmer- an efficient and user-friendly tool for extracting viral strains' k-mers from raw sequencing data

Download GUI version of StrainKmer:
Windows GUI version, Mac GUI version, Linux GUI version (Direct download)
Windows GUI version, Mac GUI version, Linux GUI version (Google drive)

Important notes:

1. Note that Mac and Linux users need to open terminal and then use command "chmod" to change the permissions of following files before using StrainDetect GUI tool:
   Mac: chmod + x StrainKmer_Mac/StrainKmer | Linux: chmod 777 StrainKmer_Linux/StrainKmer
   Mac: chmod + x StrainKmer_Mac/bin/* | Linux: chmod 777 StrainKmer_Linux/bin/*
2. Note that Mac users need to open terminal and modify ~/.zshrc file before running KMC in the StrainKmer GUI version:
   First, vi ~/.zshrc. Then, add ulimit -n 2048 to this file, save and quit. Finally, run bash ~/.zshrc

Install

Yon can install StrainKmer via Anaconda using the commands below:

git clone https://github.com/liaoherui/StrainKmer.git
cd StrainKmer
chmod 777 bin/*

conda env create -f environment.yaml
conda activate strainkmer

python StrainKmer_for_cmd.py -h

If you have installed StrainKmer and downloaded the Test_data_and_db. Then you can test StrainKmer with the example dataset using the command below.

sh test.sh

Usage

Use StrainKmer to extract k-mers from your sequencing data.

python StrainKmer_for_cmd.py -i <Input_train_dir> -d <Input_database_dir> -o <Output_dir>

Full command-line options

python StrainKmer_for_cmd.py -h

 StrainKmer - extracting viral strains' k-mers from your sequencing data.

optional arguments:
   -h,   --help                  Show help message and exit.
   -i,   SAMPLE_PATH             Sample files path.
   -d,   DATABASE_FILE_PATH      The path of pre-built database.
   -o,   OUT_PATH                The path of output files (default ./)
   -k,   K_VALUE                 K-mer length (k from 14 to 256; default: 25) 
   -ci,  CI_VALUE                Minimal K-mer occurring times (default: 2) 
   -cs,  CS_VALUE                Maximal K-mer occurring times (default: 65535)