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Tool to computationally deconvolve combinatorially pooled arrayed random mutagenesis libraries

Project description

arraylib-solve

Introduction

arraylib-solve is a tool to deconvolve combinatorially pooled arrayed random mutagenesis libraries (e.g. by transposon mutagenesis). In a typical experiment generating arrayed mutagenesis libraries, first a pooled version of the library is created and arrayed on a grid of well plates. To infer the identities of each mutant on the well plate, wells are pooled in combinatorial manner such that each mutant appears in a unique combination of pools. The pools are then sequenced using NGS and sequenced reads are stored in individual fastq files per pool. arraylib-solve deconvolves the pools and returns summaries stating the identity and location of each mutant on the original well grid. The package is based on the approach described in [1].

Installation

To install arraylib first create Python 3.8 environment e.g. by

conda create --name arraylib-env python=3.8
conda activate arraylib-env

and install the package using

pip install arraylib-solve

arraylib-solve uses bowtie2 [2] to align reads to the reference genome. Please ensure that bowtie2 is installed in your environment by running:

conda install -c bioconda bowtie2

How to run arraylib

A detailed manual how to run arraylib interactively and from the command line can be found here https://tcapraz.github.io/arraylib/index.html.

References

[1] Baym, M., Shaket, L., Anzai, I.A., Adesina, O. and Barstow, B., 2016. Rapid construction of a whole-genome transposon insertion collection for Shewanella oneidensis by Knockout Sudoku. Nature communications, 7(1), p.13270.
[2] Langmead, B. and Salzberg, S.L., 2012. Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), pp.357-359.

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