jmtsuji / tellread_format_conversion

Simple scripts for handling the output of the TELL-Read pipeline

tellread_format_conversion

Simple scripts for manipulating the format of the TELL-Read pipeline's output sequence files

All scripts can be run through the Linux command line.

Contents

add_tellread_index_to_fastq.py

Adds the index sequences (output by the TELL-Read pipeline as a separate FastQ file) to the comment line of the R1 and R2 FastQ files.

Dependencies

• python >= 3
• biopython >= 1.76

Installation

First, add the script to your PATH. Then, install all dependencies. If using conda:

conda create -n add_tellread_index_to_fastq -c conda-forge \
  python=3 biopython=1.76

conda activate add_tellread_index_to_fastq

Testing

If interested, run the automated end-to-end test with:

testing/test_add_tellread_index_to_fastq.sh \
  testing

Usage

Example usage (test data in repo):

# Assuming you are in the Github repo directory
input_dir="testing/inputs"

add_tellread_index_to_fastq.py \
  -i "${input_dir}/R1.fastq.gz" \
  -j "${input_dir}/R2.fastq.gz" \
  -k "${input_dir}/I1.fastq.gz" \
  -o "${output_dir}/${test_ID}_R1_out.fastq" \
  -p "${output_dir}/${test_ID}_R2_out.fastq"

run add_tellread_index_to_fastq.py -h for full usage instructions.