ncbigenomedownload

Tags: ncbi download genome assembly fasta genbank utility run-scope

Download assemblies and annotation files from NCBI's Assembly database.

Uses ncbi-genome-download to efficiently fetch one or more complete genome assemblies and their associated annotation and report files from the NCBI FTP site based on accession numbers, species name, or assembly ID.

Inputs

accessions: Path?

Name	Type	Description
accessions	Path?	A path to a text file containing a list of NCBI Assembly accession numbers (one per line)

Outputs

record (
    meta: Record,
    gbff: Set<Path?>,
    fna: Set<Path?>,
    rm: Set<Path?>,
    features: Set<Path?>,
    gff: Set<Path?>,
    faa: Set<Path?>,
    gpff: Set<Path?>,
    wgs_gbk: Set<Path?>,
    cds: Set<Path?>,
    rna: Set<Path?>,
    rna_fna: Set<Path?>,
    report: Set<Path?>,
    stats: Set<Path?>,
    accessions: Set<Path?>,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
gbff	Set<Path?>	GenBank format of the genomic sequence(s) (*_genomic.gbff.gz)
fna	Set<Path?>	FASTA format of the genomic nucleotide sequence(s) (*_genomic.fna.gz)
rm	Set<Path?>	RepeatMasker output for eukaryotes
features	Set<Path?>	Tab-delimited text file reporting locations and attributes for a subset of features
gff	Set<Path?>	Annotation of the genomic sequence(s) in GFF3 format (*_genomic.gff.gz)
faa	Set<Path?>	FASTA format of the accessioned protein products (*_protein.faa.gz)
gpff	Set<Path?>	GenPept format of the accessioned protein products
wgs_gbk	Set<Path?>	GenBank flat file format of the WGS master
cds	Set<Path?>	FASTA format of the nucleotide sequences corresponding to all CDS features
rna	Set<Path?>	FASTA format of accessioned RNA products
rna_fna	Set<Path?>	FASTA format of the nucleotide sequences corresponding to all RNA features
report	Set<Path?>	Tab-delimited text file reporting assembly unit names, roles, and relationships
stats	Set<Path?>	Tab-delimited text file reporting assembly statistics
accessions	Set<Path?>	The generated accession list files
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

NCBI Genome Download Parameters

Parameter	Type	Default	Description
--species	string		Name of the species to download assemblies
--accession	string		An NCBI Assembly accession to be downloaded
--accessions	string		An file of NCBI Assembly accessions (one per line) to be downloaded
--format	string	fasta	Comma separated list of formats to download
--section	string	refseq	NCBI section to download
--assembly_level	string	complete	Comma separated list of assembly levels to download
--kingdom	string	bacteria	Comma separated list of formats to download
--limit	string		Limit the number of assemblies to download
--keep_downloads	boolean	false	Save downloaded files into the bactopia-runs folder

Used By

Subworkflows

• ncbigenomedownload - Download bacterial genomes from NCBI's RefSeq database.

Workflows

• fastani - Fast alignment-free computation of whole-genome Average Nucleotide Identity.
• mashtree - Rapid phylogenetic tree construction using Mash distances.
• pangenome - Pangenome analysis with optional core-genome phylogeny.
• snippy - Rapid haplotype variant calling and core genome alignment.

Citations

If you use this in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• ncbi-genome-download
  Blin K ncbi-genome-download: Scripts to download genomes from the NCBI FTP servers (GitHub)

Source

View source on GitHub

Version

NCBIGENOMEDOWNLOAD:
    - ncbi-genome-download: 0.3.3