This article contains additional details about the workflows found in the [COVID19] workspace. You'll find a table outlining example inputs and outputs for each of the workflows listed in the workspace dashboard below.
- Getting Data into your workspace
- Sequence Data processing and assembly
- Calling lineages and clades
- NextStrain phylogenetic analysis
- All-in-one workflows
Getting Data into your workspace
| genbank_ingest | |
| Pull fasta files and metadata from NCBI Virus for SARS-CoV-2 and formats metadata for NextStrain workflows. | |
| Input | Output |
| Google_maps_api_key | Seqs_fasta |
| User_email | seqs_metadata |
| Fetch_sra_to_bam | |
|
This workflow downloads .fastq files from SRA, given an SRA_ID as input. Specifically, the output of the workflow will produce the unaligned BAM file that is needed for viral assembly. |
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| Inputs | Outputs |
|
Sra_accession |
biosample_accession |
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library_id |
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run_date |
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sample_collected_by |
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sample_collection_date |
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sample_geo_loc |
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sample_strain |
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sequencing_center |
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sequencing_platform |
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sequencing_platform_model |
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sra_metadata |
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| reads_uBAM | |
Sequence Data processing and assembly
| Fastq_to_ubam | |
|
This workflow accepts paired-end or single-end fastq files and converts them to uBAM files. |
|
|
Input |
Output |
|
fastq_1 |
"gs://test/pass1_fastq.gz" |
| fastq_2 | "gs://test/pass2_fastq.gz" |
| library_name | veroSTAT-IKO-illumina |
| platform_name | Illumina |
| platform_unit | M01472 |
| readgroup_name | A |
| run_date | 04082020 |
| sample_name | Sample1 |
| sequencing_center | Broad Institute |
| Demux_deplete | |
|
Picard-based demultiplexing and basecalling from a tarball of a raw bcl directory, followed by QC metrics and depletion. |
|
| Input | Output |
| Assemble_refbased | |
| This takes a raw read file (uBAM) and assembles a viral genome by aligning to a reference genome. | |
| Input | Output |
Calling Lineages and Clades
|
Sarscov2_lineages |
|
| Call NextClade and PANGOlin on a single SARS-CoV-2 genome | |
| Input | Output |
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Sarscov2_nextclade |
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Create NextClade visualizations on many SARS-CoV-2 genomes |
|
| Input | Output |
NextStrain Phylogenetic Analysis
|
Sarscov2_nexstrain |
|
| aligns assemblies, build trees and produces a json representation for NextStrain visualziation | |
| Input | Output |
|
genbank_curate |
|
| Pulls fasta files and metadata from NCBI Virus and formats metadata to use in Nexstrain workvlows | |
| Input | Output |
All-in-one Workflows
| Sarscov2_illumina_full | |
|
This workflow is a combination of several workflows, as illustrated in the diagram above. |
|
|
Input |
Output |
|
samplesheet |
Custom formatted tsv samplesheet |
|
spikein_db |
Spike-in fasta file |
|
author_template_sbt |
List of authors for submission to NCBI |
|
spuid_namespace |
Defaulted to Broad_GCID |
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amplicon_bed_prefix |
Amplicon primers to trim in reference coordinate space |
|
biosample_attributes |
The post-submission attributes file that is generated by NCBI after BioSample submission |
|
flowcell_tgz |
gs:// path to flowcell.tar.gz |
|
instrument_model |
Controlled vocabulary text field for instrument model |
|
reference_fasta |
Reference genome to align reads to |
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sra_title |
Title that will appear in NCBI SRA packed file (free text) |
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sample_rename_map |
Two column tsv that links the sample id assigned to sample upon receipt in lab to a reformatted sample id acceptable to NCBI |
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sarscov2_sra_to_genbank |
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| Input | Output |
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sarscov2_genbank |
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| Input | Output |