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FASTQINS is a Python pipeline to map transponson insertions from Tn-seq data.

Requirements

Specific libraries are required by FASTQINS. We provide a requirements file to install everything at once. To do so, you will need first to have pip installed and then run:

pip3 --version                      # Check if installed
sudo apt-get install python3-pip    # if you need to install pip, you can check installation with the previous command
pip3 install -r requirements.txt

In addition, we have as dependencies standard tools commonly used in high-throughput sequencing analysis:

Fastuniq
Bowtie2
Samtools
Bedtools

Path to these dependencies can still be defined by the user editing the file dependencies and reinstalling FASTQINS.

Installation & Help

Download this repository and run:

python3 setup.py install

You may require to call it using sudo. Once installed, fastqins should be available anywhere in your terminal.

In the case you need to install the package in a specific directory of your system, you can call the argument --install-lib followed by a directory path:

python3 setup.py install --install-lib /custom/path/

Example

Requirements to run an experiment are:

-i [fastq files with transposon mapped, if no -i2 is passed, single-end mapping by default]
-t [IR transposon sequence, expected to be found contiguous genome sequence]
-g [genome sequence, fasta or genbank format]
-o [output directory to locate the results]

As example, we included a pair of files that you can use to test the pipeline functioning as:

fastqins -i ./test/test_read2.fastq.gz -i2 ./test/test_read1.fastq.gz -t TACGGACTTTATC -g ./test/NC_000912.fna -o test -v -r 0

To see additional arguments:

fastqins --help

You can see here a flowchart of how FASTQINS works.

Output Information:

The following files are generated as default output:

• *_fw.qins - read counts of insertions mapping to forward strand [example]
• *_rv.qins - read counts of insertions mapping to reverse strand [example]
• *.qins - read counts of insertions mapping to both strands [example]
• *.bam - file generated with the aligned reads
• *.log - log file with general features of the process run [example]

Contact

This project has been fully developed at Centre for Genomic Regulation at the group of Design of Biological Systems.

If you experience any problem at any step involving the program, you can use the 'Issues' page of this repository or contact:

Miravet-Verde, Samuel
Lluch-Senar, Maria
Serrano, Luis

License

FASTQINS is under a common GNU GENERAL PUBLIC LICENSE. Plese, check LICENSE for further information.

[2020] - Centre de Regulació Genòmica (CRG) - All Rights Reserved*