Installation

Python-only installation

k-seq package can directly install from pip (https://pypi.org/project/k-seq/):

pip install k-seq

The python-only package has most functionalities ready-to-use for count data (e.g., preprocessed count files or a CSV table). For FASTQ read joining, trimming, and deduplication, we use EasyDIVER and require additional dependencies on PANDAseq.

Complete installation

Option 1: install with conda

We recommend to use Anaconda to create a separate k-seq environment. Or a minimal installation: Miniconda.

To crate k-seq environment once conda in installed:

# change directory to downloaded repo
cd /to/k-seq-git-repo

# create a k-seq environment
conda create -f environment.yml

# activate k-seq environment
conda activate k-seq

# install k-seq python package
pip install k-seq

Option 2: install manually

Before install k-seq python packge, please install to EasyDIVER for sequencing reads processing. Once EasyDIVER is installed, install k-seq python package through pip:

pip install k-seq