search_seq_of_interest.md

Steps to search metagenomic assemblies for a sequence of interest

1. Make reference database of sequence of interest

makeblastdb -in ${ref} -dbtype nucl -out ${ref}.db

2. Blast metagenomic assemblies against reference

blastn -query Assembly/MEGAHIT/${strain}.contigs.fa -max_target_seqs 1 -evalue 1e-10 -outfmt 6 -db ${ref}.db > blastn_${strain}

3. Parse blastn output

cat blastn_${strain} | cut -f 1,7,8 > coord.${strain}

4. Parse the fasta for the blastn contig ranges using SCGid

module load miniconda3

source SCGid/scgidenv/bin/activate 

python3 get_these_contig_ranges.py --fasta Assembly/MEGAHIT/${strain}.contigs.fa --coordinates coord.${strain} > ${strain}_${ref}.contigs