restez: Query GenBank locally

ncbi
data-access
package
software-peer-review
Tags: #<Tag:0x00007fbc54c5dd30> #<Tag:0x00007fbc54c5dbf0> #<Tag:0x00007fbc54c5dab0> #<Tag:0x00007fbc54c5d920>

#1

Author: Dom Bennett

" R packages for interacting with the National Center for Biotechnology Information (NCBI) have, to-date, depended on API query calls via NCBI’s Entrez. For computational analyses that require the automated look-up of reams of biological sequence data, piecemeal querying via bandwith-limited requests is evidently not ideal.

restez attempts to make large queries to NCBI GenBank more efficient by allowing users to download whole sections of GenBank, create a local database from these downloaded files and then query this mini-GenBank version instead."

Read the full Tech Note for more info and a short use case: https://ropensci.org/technotes/2018/12/03/restez/