extract-COI

Collection of small scripts to identify and extract candidate COI regions from tblastn result tables formatted in a specific way.

Dependencies

You need the following external software to run this workflow:

bedtools (https://github.com/arq5x/bedtools2)
ncbi-blast (https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)

You also need these python packages:

pandas
biopython

How to run

First, clone the repository and go inside the cloned directory:

git clone https://github.com/etkayapar/extract-COI
cd extract-COI

Originally the Bombyx mori COI sequence queried against input genome assemblies (it is included in this repo for you to easily test). To change the query COI sequence, replace the COI_query.fasta file with the query sequence of your choice.

To run the entire workflow, you need to have a plaintext file with absolute paths to your assemblies (one assembly for each line in the file).

Then run the workflow:

scripts/main.sh <GENOME_PATHS_FILE> <NUMBER_OF_THREADS>

After a successful run you will find your nucleotide and amino-acid COI sequences extracted in the project root directory named as:

all_COI.fa
all_COI.faa