Assembly Fetch¶
Quick Facts¶
| Workflow Type | Applicable Kingdom | Last Known Changes | Command-line Compatibility | Workflow Level |
|---|---|---|---|---|
| Data Import | Any taxa | PHB v1.3.0 | Yes | Sample-level |
Assembly_Fetch_PHB¶
The Assembly_Fetch workflow downloads assemblies from NCBI. This is particularly useful when you need to align reads against a reference genome, for example during a reference-based phylogenetics workflow. This workflow can be run in two ways:
- You can provide an accession for the specific assembly that you want to download, and
Assembly_Fetchwill run only the NCBI genome download task to download this assembly, - You can provide an assembly, and
Assembly_Fetchwill first use theReferenceSeekertask to first find the closest reference genome in RefSeq to your query assembly and then will run the NCBI genome download task to download that reference assembly.
Tip
NOTE: If using Assembly_Fetch workflow version 1.3.0 or higher, the call-caching feature of Terra has been DISABLED to ensure that the workflow is run from the beginning and data is downloaded fresh. Call-caching will not be enabled, even if the user checks the box ✅ in the Terra workflow interface.
Inputs¶
Assembly_Fetch requires the input samplename, and either the accession for a reference genome to download (ncbi_accession) or an assembly that can be used to query RefSeq for the closest reference genome to download (assembly_fasta).
This workflow runs on the sample level.
| Terra Task Name | Variable | Type | Description | Default Value | Terra Status |
|---|---|---|---|---|---|
| reference_fetch | samplename | String | Your sample's name | Required | |
| reference_fetch | assembly_fasta | File | Assembly FASTA file of your sample | Optional | |
| reference_fetch | ncbi_accession | String | NCBI accession passed to the NCBI datasets task to be downloaded. Example: GCF_000006945.2 (Salmonella enterica subsp. enterica, serovar Typhimurium str. LT2 reference genome) | Optional | |
| ncbi_datasets_download_genome_accession | cpu | Int | Number of CPUs to allocate to the task | 1 | Optional |
| ncbi_datasets_download_genome_accession | disk_size | Int | Amount of storage (in GB) to allocate to the task | 50 | Optional |
| ncbi_datasets_download_genome_accession | docker | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/staphb/ncbi-datasets:14.13.2" | Optional |
| ncbi_datasets_download_genome_accession | include_gbff | Boolean | set to true if you would like the GenBank Flat File (GBFF) file included in the output. It contains nucleotide sequence, metadata, and annotations. | FALSE | Optional |
| ncbi_datasets_download_genome_accession | include_gff3 | Boolean | set to true if you would like the Genomic Feature File v3 (GFF3) file included in the output. It contains nucleotide sequence, metadata, and annotations | FALSE | Optional |
| ncbi_datasets_download_genome_accession | memory | Int | Amount of memory/RAM (in GB) to allocate to the task | 4 | Optional |
| referenceseeker | cpu | Int | Number of CPUs to allocate to the task | 4 | Optional |
| referenceseeker | disk_size | Int | Amount of storage (in GB) to allocate to the task | 200 | Optional |
| referenceseeker | docker | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/biocontainers/referenceseeker:1.8.0--pyhdfd78af_0" | Optional |
| referenceseeker | memory | Int | Amount of memory/RAM (in GB) to allocate to the task | 16 | Optional |
| referenceseeker | referenceseeker_ani_threshold | Float | ANI threshold used to exclude ref genomes when ANI value less than this value. | 0.95 | Optional |
| referenceseeker | referenceseeker_conserved_dna_threshold | Float | Conserved DNA threshold used to exclude ref genomes when conserved DNA value is less than this value. | 0.69 | Optional |
| referenceseeker | referenceseeker_db | File | Database used by the referenceseeker tool that contains bacterial genomes from RefSeq release 205. Downloaded from referenceseeker GitHub repo. | "gs://theiagen-public-files-rp/terra/theiaprok-files/referenceseeker-bacteria-refseq-205.v20210406.tar.gz" | Optional |
| version_capture | docker | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
| version_capture | timezone | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | Optional |
Analysis Tasks¶
ReferenceSeeker (optional) Details
ReferenceSeeker¶
ReferenceSeeker uses your draft assembly to identify closely related bacterial, viral, fungal, or plasmid genome assemblies in RefSeq.
Databases for use with ReferenceSeeker are as follows, and can be used by pasting the gs uri in double quotation marks " " into the referenceseeker_db optional input:
- archea:
gs://theiagen-public-files-rp/terra/theiaprok-files/referenceseeker-archaea-refseq-205.v20210406.tar.gz - bacterial (default):
gs://theiagen-public-files-rp/terra/theiaprok-files/referenceseeker-bacteria-refseq-205.v20210406.tar.gz - fungi:
gs://theiagen-public-files-rp/terra/theiaprok-files/referenceseeker-fungi-refseq-205.v20210406.tar.gz - plasmids:
gs://theiagen-public-files-rp/terra/theiaprok-files/referenceseeker-plasmids-refseq-205.v20210406.tar.gz - viral:
gs://theiagen-public-files-rp/terra/theiaprok-files/referenceseeker-viral-refseq-205.v20210406.tar.gz
For ReferenceSeeker to identify a genome, it must meet user-specified thresholds for sequence coverage (referenceseeker_conserved_dna_threshold) and identity (referenceseeker_ani_threshold). The default values for these are set according to community standards (conserved DNA >= 69 % and ANI >= 95 %). A list of closely related genomes is provided in referenceseeker_tsv. The reference genome that ranks highest according to ANI and conserved DNA values is considered the closest match and will be downloaded, with information about this provided in the assembly_fetch_referenceseeker_top_hit_ncbi_accession output.
ReferenceSeeker Technical Details
| Links | |
|---|---|
| Task | task_referenceseeker.wdl |
| Software version | 1.8.0 ("us-docker.pkg.dev/general-theiagen/biocontainers/referenceseeker:1.8.0--pyhdfd78af_0") |
| Software Source Code | https://github.com/oschwengers/referenceseeker |
| Software Documentation | https://github.com/oschwengers/referenceseeker |
| Original Publication(s) | ReferenceSeeker: rapid determination of appropriate reference genomes |
NCBI Datasets Details
NCBI Datasets¶
The NCBI Datasets task downloads specified assemblies from NCBI using either the virus or genome (for all other genome types) package as appropriate.
NCBI Datasets Technical Details
| Links | |
|---|---|
| Task | task_ncbi_datasets.wdl |
| Software version | 14.13.2 (us-docker.pkg.dev/general-theiagen/staphb/ncbi-datasets:14.13.2) |
| Software Source Code | https://github.com/ncbi/datasets |
| Software Documentation | https://github.com/ncbi/datasets |
| Original Publication(s) | Not known to be published |
Outputs¶
| Variable | Type | Description |
|---|---|---|
| assembly_fetch_analysis_date | String | Date of assembly download |
| assembly_fetch_ncbi_datasets_assembly_data_report_json | File | JSON file containing report about assembly downloaded by Asembly_Fetch |
| assembly_fetch_ncbi_datasets_assembly_fasta | File | FASTA file downloaded by Assembly_Fetch |
| assembly_fetch_ncbi_datasets_docker | String | Docker file used for NCBI datasets |
| assembly_fetch_ncbi_datasets_gff | File | Assembly downloaded by Assembly_Fetch in GFF3 format |
| assembly_fetch_ncbi_datasets_gff3 | File | Assembly downloaded by Assembly_Fetch in GFF format |
| assembly_fetch_ncbi_datasets_version | String | NCBI datasets version used |
| assembly_fetch_referenceseeker_database | String | ReferenceSeeker database used |
| assembly_fetch_referenceseeker_docker | String | Docker file used for ReferenceSeeker |
| assembly_fetch_referenceseeker_top_hit_ncbi_accession | String | NCBI Accession for the top it identified by Assembly_Fetch |
| assembly_fetch_referenceseeker_tsv | File | TSV file of the top hits between the query genome and the Reference Seeker database |
| assembly_fetch_referenceseeker_version | String | ReferenceSeeker version used |
| assembly_fetch_version | String | The version of the repository the Assembly Fetch workflow is in |
References¶
ReferenceSeeker: Schwengers O, Hain T, Chakraborty T, Goesmann A. ReferenceSeeker: rapid determination of appropriate reference genomes. J Open Source Softw. 2020 Feb 4;5(46):1994.
NCBI datasets: datasets: NCBI Datasets is an experimental resource for finding and building datasets [Internet]. Github; [cited 2023 Apr 19]. Available from: https://github.com/ncbi/datasets