compile_genbank: Compile Sequence and Metadata for GenBank Submission

In CUGBF/deidentifiedDB: Utility to Manage Clemson University COVID-19 Surveillance Data

Compile Sequence and Metadata for GenBank Submission

Description

Compile Sequence and Metadata for GenBank Submission

Usage

compile_genbank(
  testkit_ids,
  seq_dir,
  sample_collection_tbl = NULL,
  demographics_tbl = NULL,
  viralrecon_tbl = NULL,
  deidentifiedDB = NULL
)

Arguments

testkit_ids	Testkit IDs to include in the GenBank Submission
seq_dir	Directory containing FASTA files of consensus sequence for individual samples
sample_collection_tbl	Path to the tibble containing sample collection data
demographics_tbl	Path to the tibble containing demographics data
viralrecon_tbl	Path to the tibble containing viralrecon results
deidentifiedDB	Path to the deidentifiedDB SQLite File

Value

List of three elements: 'int_tbl' : Tibble for internal use, 'ext_tbl' : Tibble containing metadata required by GenBank, 'seqs' : DNAStringSet with consensus sequences for each Sequence_ID

CUGBF/deidentifiedDB documentation built on Sept. 13, 2023, 6:28 a.m.