Bioinformatic scripts to analyze ITS (Internal transcribed spacer) sequences to identify Mucorales order fungi.
Files:
- its_pipeline.sh: main bash script to analyze FASTA sequences
- blast_result_parser.py: Python 3 script to filter out BLAST hits
Analysis steps:
Notes:
- This pipeline assumes that seqs file names and seq headers are the same.
- For example, Sample file name: ERR789.fasta, Sample fasta header: >ERR789
- All individual seq files are stored in the "./seqs" directory
Used Command Line Programs:
- Seqkit, Blast, MAFFT, and Iqtree2
Many thanks to Esra Merdan for creating the illustration for this project.