Summarizing list of Genbank Assembly Accessions

Question

[fheller]

I have a list of genbank accession ID numbers resulting from an experiment. I'm interested in summarizing the strains to which they belong, eg by grouping them at a genus or species level. Does anyone know of a tool me to do this? Initially I thought I could use something like phyloT (https://phylot.biobyte.de), but my IDs are in the wrong format. Any suggestions as to tools I might look into or search terms I might use to explore further myself would be greatly appreciated.

Examples of the sort of Genbank Assembly Accessions I have: GCA_013300845.1 GCA_014847545.1 GCA_004167785.1

Answer 1

[GenoMax]

Using EntrezDirect:

$ more id
GCA_013300845.1
GCA_014847545.1
GCA_004167785.1

$ epost -db assembly -format acc -input id | esummary | xtract -pattern DocumentSummary -element Genbank,Organism,Sub_type,Sub_value
GCA_014847545.1 Ligilactobacillus ruminis (firmicutes)
GCA_013300845.1 Blautia glucerasea (firmicutes) strain  MSK.20.42
GCA_004167785.1 Bacteroides ovatus (CFB group bacteria) strain  am_0171