Useful Blast Commands and one-liners

 # Blast command with additional details such as query length and subject length

blastn -db /storage/data/Storage/nt/nt/nt -query query.fa -outfmt '6 qseqid sseqid pident nident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen' -out query.fa_vs_nt_with_stitle_blastresults.txt -num_threads 48

# To get title of subject, For example: Enterobacter_aerogenes_strain_G7,_complete_genome 

blastn -db /storage/data/Storage/nt/nt/nt -query query.fa -outfmt '6 qseqid sseqid pident nident length mismatch gapopen qstart qend sstart send evalue bitscore stitle qlen slen' -out query.fa_vs_nt_with_stitle_blastresults.txt -num_threads 48

# Tophits

$ awk '!x[$1]++' query.fa_vs_nt_with_stitle_blastresults.txt

# Tophits with plasmid assignment

$ awk '!x[$1]++' query.fa_vs_nt_with_stitle_blastresults.txt | sed 's/ /_/g' | awk '{print $0 "\t" $5*100/$(NF-1)}' | column -t | grep 'plasmid'