Extracting taxonomic lineages from NCBI based on assembly_summary files

This tool is used to create files for use with sourmash tax and sourmash lca index, for taxonomic summaries. The tool starts by taking in an assembly summary file, and ends with an output file format like so:

accession,taxid,superkingdom,phylum,class,order,family,genus,species,strain
AAAC01000001,191218,Bacteria,Firmicutes,Bacilli,Bacillales,Bacillaceae,Bacillus,Bacillus anthracis,
AABL01000001,73239,Eukaryota,Apicomplexa,Aconoidasida,Haemosporida,Plasmodiidae,Plasmodium,Plasmodium yoelii,
AABT01000001,285217,Eukaryota,Ascomycota,Eurotiomycetes,Eurotiales,Aspergillaceae,Aspergillus,Aspergillus terreus,
AABF01000001,209882,Bacteria,Fusobacteria,Fusobacteriia,Fusobacteriales,Fusobacteriaceae,Fusobacterium,Fusobacterium nucleatum,

Snakestart: a snakemake workflow

Install snakemake, and run it:

snakemake

This will generate an output file example.lineages.csv based on the input file example.assembly_summary.txt. Note that snakemake will download all of the necessary support files too!

Code based on https://github.com/dib-lab/2018-ncbi-lineages.

CTB 20.4.2022