snippy_core

Tags: snippy core-genome alignment phylogeny snp bacteria run-scope

Core-SNP alignment from Snippy outputs.

Uses Snippy to generate a core genome alignment from multiple Snippy outputs. It combines variant calls (VCF) and alignments to produce a core SNP alignment, which can be used for phylogenetic analysis.

Inputs

record (
    meta: Record,
    _vcf: Set<Path>,
    _aligned_fa: Set<Path>
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
_vcf	Set<Path>	List of VCF files from Snippy
_aligned_fa	Set<Path>	List of aligned FASTA files from Snippy

Field	Type	Description
meta	Record	Groovy Record containing reference information
reference	Path	Reference genome (FASTA or GenBank format)

reference: Path
mask: Path?

Name	Type	Description
mask	Path?	BED file of regions to mask in the alignment

Outputs

record (
    meta: Record,
    supplemental: Set<Path>,
    aln: Path,
    full_aln: Path,
    clean_full_aln: Path,
    tab: Path,
    vcf: Path,
    txt: Path,
    samples: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
supplemental	Set<Path>	Supplemental files including individual sample alignments
aln	Path	A core SNP alignment in FASTA format
full_aln	Path	A whole genome SNP alignment (includes invariant sites)
clean_full_aln	Path	A whole genome SNP alignment (includes invariant sites) with Ns
tab	Path	Tab-separated list of core SNP sites with alleles (no annotations)
vcf	Path	Multi-sample VCF file with genotype GT tags for all discovered alleles
txt	Path	Tab-separated list of alignment and core-size statistics
samples	Path	List of samples included in the core alignment
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

Snippy-Core Parameters

Parameter	Type	Default	Description
--snippy_core_maxhap	integer	100	Largest haplotype to decompose
--snippy_core_mask	string		BED file of sites to mask
--snippy_core_mask_char	string	X	Masking character
--snippy_core_opts	string		Extra options in quotes for snippy-core

Used By

Subworkflows

• snippy_core - Generate core-genome SNP alignment from per-sample Snippy outputs.

Workflows

• 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)

• Snippy
  Seemann T Snippy: fast bacterial variant calling from NGS reads (GitHub)

• BCFtools
  Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H Twelve years of SAMtools and BCFtools GigaScience Volume 10, Issue 2 (2021)

• Bedtools
  Quinlan AR, Hall IM BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010)

• freebayes
  Garrison E, Marth G Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] (2012)

• Seqtk
  Li H Toolkit for processing sequences in FASTA/Q formats (GitHub)

• SnpEff
  Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Douglas M A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6(2), 80-92 (2012)

• VCF-Annotator
  Petit III RA VCF-Annotator: Add biological annotations to variants in a VCF file. (GitHub)

• Vcflib
  Garrison E Vcflib: A C++ library for parsing and manipulating VCF files (GitHub)

• vt
  Tan A, Abecasis GR, Kang HM Unified representation of genetic variants. Bioinformatics 31(13), 2202-2204 (2015)

Source

View source on GitHub

Version

SNIPPY_CORE:
    - bactopia-variants: 1.0.4