EntrezDownload: Download Public Sequence Data

In carolinafishes/toast: Transcriptome Ortholog Alignment Sequence Tools

Download Public Sequence Data

Description

Utility for downloading sequence data from NCBI for a user specified group of organisms

Usage

EntrezDownload(txid, fasta_dir, minimumSeq = 350, maximumSeq = NULL)

Arguments

txid	NCBI taxon ID. See https://ncbi.nlm.nih.gov and manual
fasta_dir	Place to store fasta sequences. Must end with */fasta/
minimumSeq	Minimum number of sequences a species must have to bother downloading defaults to 350
maximumSeq	Maximum number of sequences to download per species. Useful for testing scripts and troubleshooting TOAST/BUSCO

Value

Returns graphic of missing data based on defined threshold

Author(s)

Dustin J Wcisel, [e-mail]

James Thomas Howard, [e-mail]

Jeffrey A Yoder, [e-mail]

Alex Dornburg, [e-mail]

Examples

SequenceDownload(txid = 9721, fasta_dir = "path/to/fasta/", minimumSeq = 350)

carolinafishes/toast documentation built on April 12, 2025, 10:41 a.m.