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Jupyter notebook to assist wet lab shotgun pipeline

License: MIT License

Jupyter Notebook 99.37% Python 0.63%

metagenomics_pooling_notebook's Introduction

metagenomics_pooling_notebook

A Jupyter notebook to assist wet lab shotgun pipeline.

Installation

To install this notebook, first clone the repository from GitHub:

git clone https://github.com/tanaes/metagenomics_pooling_notebook.git

Create a Python3 Conda environment in which to run the notebook:

conda create -n pooling_nb python=3

Activate the Conda environment:

source activate pooling_nb

Change directory to the downloaded repository folder and install:

cd metagenomics_pooling_notebook
pip install -e .

Finally, to enable the notebook Table of Contents, activate the required nbextensions:

jupyter contrib nbextension install --sys-prefix --skip-running-check
jupyter nbextension enable toc2/main

Use

The notebook itself contains detailed usage instructions.

Ideally, you will copy this original notebook and use it for each plate you create with the shotgun pipeline.

Just make sure to activate the right Conda environment before starting the notebook.

Here's a quick example:

cp metagenomics_pooling.ipynb ~/New_project/new_project_pooling.ipynb
cd ~/New_project
source activate pooling_nb
jupyter notebook

metagenomics_pooling_notebook's People

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c1carpenter stephanieorch unique-identifier eldeveloper

metagenomics_pooling_notebook's Issues

Sample Sheet generator module not recognizing RapidRun2500 as sequencing platform.

The sample sheet generator should recognize RapidRun2500 as a sequencing platform. This sequencing platform does NOT need the i5 index to be revcomped.

Allow different source plates for DNA normalization picklist

Support for Library Prep on 192 format.

The notebook should support the option of making a 192 format normalized DNA plate given appropriate sample maps and quant data.
I've attached Quant data and Sample maps for CF strains plates 1-2.

The goal of adding 192 format support is to reformat samples into the first half of the destination plate regardless of where the source well of each samples is.

Make split-plate visualization of DNA concentrations

Add export of combined dataframe

SampleSheet generation tab delimited bug

The column headers for [Data] aspect of the sample sheet is still tab delimited after specifying , as delimiter.

CF_1-2_samplesheet.xlsx

Add parser for stats output from demultiplexing and visualization

We don't really need to run samples through total QC to get a quick estimate of evenness and demuxing stats. Might as well import this in bottom of notebook to do immediate gut-check evals.

Input norm module can't handle '?????' as reported concentration

The automated quant procedure we use will occasionally output '?????' as the reported concentration. This means that the sample was outside the detection window. The script should be able to handle '????' and treat them as '0'.

Add visual indicator for sample sheet generation if i5 barcode is revcomped

This will help develop intuition for sequencer:revcomp requirements, and hopefully limit the number of mistakes leading to re-runs

Check for duplicates in sample names for sample sheet

Address barcode r/c by sequencer type in sample sheet generation

min_conc pooling value

Notebook should pool samples that don't meet min_conc at 100nL instead of 0nL.

Max_vol_per_well function in pooling pick list can't handle nan values

The max_vol_per_well function failed to cycle to the next well when exceeding max vol. After inspecting the transfer volumes, I have the belief that it's an error that was introduced by nan values being present in the pooling volumes. Nan values throw off the function.
Attached is the faulty pooling pick list.
2017-11-22_FinRisk_5-8_81-83_lisas_normpool.txt

Add RKL_ default to experiment name in sample sheet

Add PDF display for pre- and post-size-selection tapestation results

This is important for consolidating records and evaluation of fragmentation over time

Add floating Table of Contents to aid navigation

potential source code: nbextensions

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