ColinAnthony / NGS_processing_pipeline

NGS_processing_pipeline

Overview:

This pipeline

1. Creates the required file structure
2. Demultiplexes sequences based on the presence of a primer
3. Does other things

Setup process:

1. Clone the git repository
2. etc

Dependecies:

Data from PrimerID workflow

1) Motifbinner
2) contam repo
3) pyhton3
4) scipy?
5) pandas
6) numpy
7) Biopython?  
if calling the pipeline using demultiplex.py,
    you will need to specify the config.json settings file and
    a primer description csv file
    Templates for these are located in the repo as template_demultiplex_config.json and
    template_master_primer_file.csv

To run:

python3 demultiplex.py --config_file <config.json> --output_dir <output directory>

Using the config file:

The configuration for the run is stored in a JSON file for reproducibility. An example file is provided which can be edited to suit your run.

The JSON file contains:

input_data

• fwd_fastq_file - This is the fastq file containing the forward (R1) sequences.

• rev_fastq_file - This is the fastq file containing the reverse (R2) sequences.

• primer_csv - This file contains the primers and their associated gene regions, as well as information on whether the sequences are overlapping, and the length of sequence preceding the primer in the fastq file.

• patient_list - This is a python list containing the patient / sample name.

• out_folder - This is the full path to the output folder.

  pipelineSettings

• out_prefix: The prefix name of your outfile.

• frame: The reading frame (1, 2 or 3).

• stops: Remove sequences with stop codons?

• min_read_length: The minimum read length.

• run_step: The step at which to resume the analysis if it is interrupted.

  haplotype_settings

• infile: The path and name of the aligned fasta file.

• field: The field that differentiates your samples/time points (use the last field if multiple. ie: 4 for 'CAP177_2000_004wpi_V3C4_GGGACTCTAGTG_28, or 2 for SVB008_SP_GGTAGTCTAGTG_231).

• script_folder: The path to the folder containing the pipeline scripts.

Output:

The output of this pipeline is X in Y format