BLAST - find 18s & 28s in genome assembly

BLAST_18s-28s_hydra.sh

Script name: BLAST_18s-28s_hydra.sh

This script is meant to help identify and extract contigs/scaffolds containing the 18s and 28s genes.

To download the script:

wget https://raw.githubusercontent.com/dmacguigan/SI-Ocean-DNA/refs/heads/main/scripts/Hydra/BLAST_Hydra/BLAST_18s-28s_hydra.sh

Try running bash batchRenameFiles.sh -h to print the help documentation.

Script to find and rename contigs/scaffolds containing
18s and/or 28s genes

author: Dan MacGuigan
contact: macguigand@si.edu

Options:
c   FASTA file containing genomics scaffolds or contigs
i   sample ID, will be used to name resulting files and BLAST hits
s   FASTA file containing query 18s sequence
l   FASTA file containing query 28s sequence
h   Print this Help

Usage:
bash BLAST_18s-28s_hydra.sh -c my_contigs.fasta -i my_sample_ID -s my_18s.fasta -l my_28s.fasta

BLAST_job.sh

Script name: BLAST_job.sh

source code

This script is a wrapper for BLAST_18s-28s_hydra.sh, allowing you analyze multiple genome assemblies.

To download the script:

wget https://raw.githubusercontent.com/dmacguigan/SI-Ocean-DNA/refs/heads/main/scripts/Hydra/BLAST_Hydra/BLAST_job.sh

You will then need to modify the INPUTS section.

# INPUTS ################################################

# working directory containing contig/scaffold FASTA files
DIR="/pool/public/genomics/macguigand/BLAST_testing/scaffolds"

# FASTA file suffix (e.g. "fasta", "fa", "fas")
# must be the same for all files in DIR
SUFFIX="fasta"

# full path to 18s and 28s query sequences
rRNA_S="/pool/public/genomics/macguigand/BLAST_testing/18s.fasta"
rRNA_L="/pool/public/genomics/macguigand/BLAST_testing/28s.fasta"

# full path to your copy of the BLAST_18s-28s_hydra.sh script
BLAST_SCRIPT="/pool/public/genomics/macguigand/BLAST_testing/BLAST_18s-28s_hydra.sh"

Running qsub BLAST_job.sh will submit the script to the cluster’s job scheduler.

Once complete, BLAST hits will be written to a new folder BLAST_hits within DIR.