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.
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.
- python >= 3
- biopython >= 1.76
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
If interested, run the automated end-to-end test with:
testing/test_add_tellread_index_to_fastq.sh \
testing
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.