Skip to content

Latest commit

 

History

History
17 lines (9 loc) · 1.09 KB

README.md

File metadata and controls

17 lines (9 loc) · 1.09 KB

BOLDigger2_batch

Submission of multi-fasta file containing cox1 sequences to BOLDigger2 via slurm HPC.

Usage: sbatch boldigger2.sh [path/to/cox1.fasta] [username] [password] [path/to/output_dir]

  • path/to/cox1.fasta = path to directory with multi-fasta file containing cox1 sequences to query against BOLD DB (.fasta must have 'cox1' in filename).
  • username = BOLD username
  • password = BOLD password
  • path/to/output_dir = path to directory to output BOLDigger2 results. Will create output_dir if it does not already exist.

BOLDigger2 multi-fasta prep script (1_BD2_prep.py)

Integrated into boldigger.sh (must be in same directory as boldigger.sh). Prepares multi-fasta file containing cox1 sequences by cleaning sequence headers, removing headers if no sequence is present, removing leading and trailing invalid characters (e.g. '-' and '~'), converting 'internal' invalid characters to 'Ns', and removing sequences <80bp. Script will append 'cleaned_' to start of input cox1.fasta file, which will be used for submission to BOLDigger2.