genomedl
Tags: download ncbi datasets genome assembly refseq sample-scope
Download genome assemblies from NCBI Datasets.
This subworkflow downloads genome assemblies using genome-dl, which resolves accessions to their latest version and subsamples species queries before fetching files from the NCBI FTP site. The downloaded assemblies are fanned out into per-genome records for downstream analysis, and the first assembly is exposed separately for use as a reference genome.
Take
accessions: Path?
| Name | Type | Description |
|---|---|---|
accessions | Path? | A file containing NCBI Assembly accessions, one per line. May be combined with the --accession and --species parameters. |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
fna | Genomic nucleotide sequences in FASTA format |
gbff | GenBank format genome sequences |
wgs_gbk | WGS master records in GenBank format |
gff | Genome annotations in GFF3 format |
gtf | Genome annotations in GTF format |
faa | Protein sequences in FASTA format |
gpff | Protein sequences in GenPept format |
cds | CDS nucleotide sequences in FASTA format |
translated_cds | CDS protein sequences in FASTA format |
rna | RNA feature nucleotide sequences in FASTA format |
features | Feature table with locations and attributes |
report | Assembly report with unit and sequence relationships |
stats | Assembly statistics |
metadata | NCBI Datasets metadata for each downloaded assembly |
summary | Human-readable run summary of the version, parameters, and results |
json | Machine-readable run report of the parameters, results, and per-assembly metadata |
run_outputs
No run-scope outputs.
Downstream Inputs
The following emissions are meant to be used as inputs to downstream subworkflows.
assemblies
| Output | Description |
|---|---|
fna | Individual downloaded assembly in FASTA format |
reference
First downloaded genome for use as a reference. Prefers GenBank (--format genbank) over FASTA, since annotation-aware consumers such as Snippy require a GenBank reference.
Module Composition
This subworkflow calls the following modules:
- genomedl - Download genome assemblies and annotation files from NCBI Datasets.
Used By
This subworkflow is used by the following 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) -
genome-dl
Petit III RA genome-dl: Download genomes from NCBI Datasets (GitHub)