katorke / fastqcs3

Main Repo for CHEM E 545/546 Final Project

FastQCS3: Fast Quantitative Checking of 16S Gene Sequencing

Main Repo for CHEM E 545/546 Final Project

Overview/Purpose

The purpose of this software is to give users a tool to quickly run quality checking immediately after sequencing results become available. The software will be designed to be a python installable package that is run from the command line. Designed modularly, the user will have the chance to specify what kind of FastQCS3 they want to perform.

Installing Dependencies

This package relies on QIIME2, a previously published microbiome analysis package, to pre-process input data and provide sequencing quality metrics. FastQCS3 seeks to utilize QIIME2 data processing capabilities while focusing on building an interactive dashboard with more useful visualization tools than QIIME2's .qza formats. To be able to utilize FastQCS3, QIIME2 must be installed first.

Installing Miniconda

You can follow the instructions here to install Miniconda.

Updating Miniconda

conda update conda

Installing wget

conda install wget

If conda install wget doesn't work, you can also try using pip install wget, sudo apt-get install wget, or use package managers like homebrew to brew install wget.

If you have a Mac OS...

wget https://data.qiime2.org/distro/core/qiime2-2020.11-py36-osx-conda.yml

conda env create -n qiime2-2020.11 --file qiime2-2020.11-py36-osx-conda.yml

rm qiime2-2020.11-py36-osx-conda.yml

If you have a Windows OS on Linux...

wget https://data.qiime2.org/distro/core/qiime2-2020.11-py36-linux-conda.yml

conda env create -n qiime2-2020.11 --file qiime2-2020.11-py36-linux-conda.yml

rm qiime2-2020.11-py36-linux-conda.yml

If you have a Windows OS...

the process to install wget will be a more complicated. You'll have to download wget and move the correct exe files into your correct system directories as shown here.

This can be complicated if you don't already have administrator privileges set up in these files on your machine; we recommend using the Mac OS or Windows Subsystem for Linux. Instructions on installing Windows subsystem for Linux can be found [here] (https://docs.microsoft.com/en-us/windows/wsl/install-win10).

To activate your environment,

conda activate qiime2-2020.11

You can deactivate at any time with conda deactivate.

From QIIME2 to FastQCS3

Include explanation of Nick's files that automate QIIME2 processing?