BOL: Bash command to explore assembly summary genbank !

BioScripts
Neelam Jha
Bash command to explore assembly summary genbank !

Bash command to explore assembly summary genbank !

By Neelam Jha 761 days ago

wget https://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt

pip3 install csvkit

csvcut -t -K 1 -c 'excluded_from_refseq' assembly_summary_genbank.txt \
  | tail -n +2 | tr ";" "\n" \
    | sed -e 's/^ //' -e 's/ $//' | grep -v '""' \
      | sort | uniq -c | sort -nr