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Workflows available

Assembly_Fetch

Augur

BaseSpace_Fetch

Cauris_CladeTyper

Concatenate_Column_Content

Core_Gene_SNP

Create_Terra_Table

CZGenEpi_Prep

Find_Shared_Variants

Freyja Workflow Series

GAMBIT_Query

Kraken2

kSNP3

Lyve_SET

MashTree_FASTA

Mercury_Prep_N_Batch

NCBI-AMRFinderPlus

Pangolin Update

RASUSA

Rename_FASTQ

Samples_to_Ref_Tree

Snippy_Streamline

Snippy_Streamline_FASTA

Snippy_Tree

Snippy_Variants

SRA_Fetch

TBProfiler_tNGS

Terra_2_GISAID

Terra_2_NCBI

TheiaCoV Workflow Series

TheiaEuk

TheiaMeta

TheiaProk Workflow Series

TheiaValidate

Transfer_Column_Content

Usher_PHB

VADR_Update

Zip_Column_Content

Overview

The Lyve_SET WDL workflow runs the https://github.com/lskatz/lyve-SET pipeline developed by Lee Katz et al. for phylogenetic analysis of bacterial genomes using high quality single nucleotide polymorphisms (hqSNPs). The Lyve_SET workflow identifies SNPs amongst a set of samples by mapping sequencing reads to a reference genome, identifying high quality SNPs, and inferring phylogeny using RAxML.

Lyve-SET Pipeline (from Lyve-SET paper)

Inputs

Required User Inputs

Optional User Inputs

Tasks/Actions

The Lyve_SET WDL workflow is run using read data from a set of samples. The workflow will produce a pairwise SNP matrix for the sample set and a maximum likelihood phylogenetic tree. Details regarding the default implementation of Lyve_SET and optional modifications are listed below.

1. Read processing
   1. By default, the Lyve_SET WDL workflow will perform read cleaning using the CG-Pipeline “CGP”. However, read cleaning can be turned off or performed using “BayesHammer” using the read_cleaner input variable.
2. Reference procurement
   1. By default, the Lyve_SET WDL workflow will not mask phages or cliffs in the reference genome. Cliffs refer to regions of the reference genome where read coverage rises or falls abruptly. Masking phages and cliffs is intended to remove low quality SNPs. Users can invoke phage and cliff masking by setting the mask_cliffs and mask_phages variables to “true”.
3. SNP discovery
   1. The Lyve_SET WDL workflow uses the default read mapper and variant caller from the Lyve-SET pipeline (smalt and varscan). Additional options for each are available using the mapper and snpcaller input variables.
   2. The workflow also uses the default parameters for variant calling from the Lyve-SET pipeline: the minimum percent consensus to call a base is 0.75 and minimum read depth is 10X. These parameters can be manually modified using the min_alt_frac and min_coverage input variables.
4. Phylogenetic analysis
   1. The Lyve_SET workflow will attempt to produce a multiple sequence alignment, SNP distance matrix, and phylogenetic tree. These actions can be skipped by indicating nomsa = true, nomatrix = true, or notrees = true, respectively.

Outputs

For full descriptions of Lyve-SET pipeline outputs, we recommend consulting the Lyve-SET documentation: https://github.com/lskatz/lyve-SET/blob/master/docs/OUTPUT.md

The following output files are populated to the Terra data table. However, please note that certain files may not appear in the data table following a run for two main reasons:

1. The user instructed the workflow to skip an analysis step
   1. For example, if notrees = true, no tree file will appear
2. The workflow skipped an analysis step due to an issue with the input data

Outputs

In addition to these outputs, all of the files produced by the Lyve-SET pipeline are available in the task-level outputs, including intermediate files and individual bam and vcf files for each sample. These files can be accessed viewing the execution directory for the run.

References