README.md

pyinseq

Lightweight package to map transposon insertion sequencing (INSeq) data in bacteria.

Documentation

See the pyinseq documentation.

Quickstart

Installation

1. Download (or git clone) the pyinseq package using the link on this page.

2. Install the Anaconda Python 3.5 download.

3. In the command line run the command below to install additional packages as detailed in the requirements.txt file.
   pip install -r requirements.txt

Run the simple example dataset to check installation

$ python scripts/pyinseq.py -i data/example/example01.fastq -s data/example/example01.txt -g data/example/ES114v2.gb -e example01

Required arguments

-i --input - Illumina reads file in FASTQ format

-s --samples - sample list where each line is the sample_nametabbarcode(4bp)

-g --genome - concatenated genbank file for all contigs for the genome

-e --experiment - all results files will be created in the subfolder of this name

Optional arguments

-d --disruption - fraction of gene disrupted (0.0 - 1.0)

Full documentation