README.md

hspipeline

hspipeline connects existing tools together to analyse high-throughput sequencing data.

hspipeline is a command-line tool. Run it without arguments to see instructions and a detailed description of the arguments.

Upon execution, hspipeline will first check to see if all necessary tools are on the path and will exit if they can't be found.

Tools needed to run the pipeline

Make sure the following tools are compiled and available on your system PATH:

• bcftools
• bowtie2
• samtools
• htslib
• sickle

Directory structure

Each fastq file (or pair of fastq files for paired-end reads) should go in a directory named after its sample name. All the sample folders should go into a project directory. All of the project directories should go into a top-level directory. See diagram below.

    top-level directory
    |
    +----project1
         |
         +----Sample_1
         |    |
         |    +----sample1_R1.fastq.gz
         |    |
         |    +----sample1_R2.fastq.gz
         |
         +----Sample_2  
         |    |
         |    +----sample2_R1.fastq.gz
         |    |
         |    +----sample2_R2.fastq.gz
         |
         ...
         |
         +----Sample_N

Server setup

To install hspipeline on an apache2 server running on Ubuntu (might need to modify some commands if using a different OS):

1. Install apache2

   $ sudo apt-get install apache2 apache2-utils libexpat1 ssl-cert python
   

2. Install the mod_wsgi module:

   $ sudo apt install libapache2-mod-wsgi
   

3. Symlink web/hspipeline.conf to apache's sites-available folder and enable it.

   $ sudo ln -s /path/to/hspipeline.conf /etc/apache2/sites-available
   $ sudo a2ensite /etc/apache2/sites-available/hspipeline.conf
   

4. Symlink the hspipeline folder to /var/www

   $ sudo ln -s /path/to/hspipeline /var/www
   

5. Disable the default site

   $ suddo a2dissite 000-default.conf
   

6. Create a top-level folder and make it readable/writable by everyone

   $ mkdir ~/seq_data
   $ chmod a+w ~/seq_data
   

7. Update the Paths class (located in web/paths.py) to point to the location of the various folders.

8. Restart apache

   $sudo apache2ctl restart
   

9. The site should be available at your_domain/hspipeline

Docker

To run hspipeline as a docker container:

1. Install docker

2. Make a directory to hold the sequence data somewhere on your computer (this is the "top-level directory" in the Directory structure diagram).

3. Move your project-level directory into the top-level directory.

4. Make the top-level directory and everything in it world-writable (apache runs as user 'www-data' and needs to write to these folders).

   $ chmod -R a+w /path/to/top_level_directory
   

5. Build and run docker in hspipeline folder:

   $ docker build docker
   $ docker run -it -p 9876:80 \
                --mount type=bind,source=<location on computer>,target=/seq_data \
                <image hash>
   

NOTE: If you want to use symlinks instead of copies of your data files, you need to mount the directories containing the original (unlinked) data as well so that the links will be valid inside the docker environment.

Symbols in plots

(until I add legends...)

Coverage plots

• Magenta points = Less than 5 reads for that position.

anc/evo coverage ratio plots

• Orange X = No reads in evolved strain

• Purple X = No reads in ancestor strain

• Cyan X = No reads in either strain

• Red circles = Point is > x sds away from mean ratio for that chromosome (x = 3 by default).