snippy_run

Tags: snippy variant-calling snp indel alignment bacteria sample-scope

Rapid haploid variant calling and core genome alignment.

Uses Snippy to find SNPs and indels between a haploid reference genome and your Next-Generation Sequencing (NGS) sequence reads. It maps reads to the reference, calls variants, and generates a consensus sequence.

Uses explicit positional record fields for reads:

• Input: record(meta, r1, r2, se) where each read slot is Path?

Inputs

record (
    meta: Record,
    r1: Path?,
    r2: Path?,
    se: Path?
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
r1	Path?	Illumina R1 reads (paired-end)
r2	Path?	Illumina R2 reads (paired-end)
se	Path?	Single-end Illumina reads

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

Outputs

record (
    meta: Record,
    aligned_fa: Path?,
    vcf: Path?,
    aligned_fa_error: Path?,
    vcf_error: Path?,
    error: Path?,
    annotated_vcf: Path,
    bam: Path?,
    bai: Path?,
    bed: Path,
    consensus_fa: Path,
    consensus_subs_fa: Path,
    consensus_subs_masked_fa: Path,
    coverage: Path,
    csv: Path,
    filt_vcf: Path,
    gff: Path,
    html: Path,
    raw_vcf: Path,
    subs_vcf: Path,
    tab: Path,
    txt: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
aligned_fa	Path?	A version of the reference with - at zero coverage positions
vcf	Path?	The final annotated variants in VCF format
aligned_fa_error	Path?	Aligned FASTA file generated during error state
vcf_error	Path?	VCF file generated during error state
error	Path?	Error log text file
annotated_vcf	Path	Annotated VCF file
bam	Path?	The alignments in BAM format (includes unmapped/multimapping)
bai	Path?	Index for the BAM file
bed	Path	The variants in BED format
consensus_fa	Path	Reference genome with all variants instantiated
consensus_subs_fa	Path	Reference genome with only substitution variants instantiated
consensus_subs_masked_fa	Path	Reference genome with substitutions instantiated and low coverage masked
coverage	Path	Per-base coverage depth information
csv	Path	A comma-separated summary of variants
filt_vcf	Path	The filtered variant calls from Freebayes
gff	Path	The variants in GFF3 format
html	Path	A HTML summary of the variants
raw_vcf	Path	The unfiltered variant calls from Freebayes
subs_vcf	Path	VCF containing only substitution variants
tab	Path	A simple tab-separated summary of all variants
txt	Path	Tab-separated columnar list of alignment statistics
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 Run Parameters

Parameter	Type	Default	Description
--reference	string		Reference genome in GenBank format
--snippy_mapqual	integer	60	Minimum read mapping quality to consider
--snippy_basequal	integer	13	Minimum base quality to consider
--snippy_bwaopt	string		Extra BWA MEM options, eg. -x pacbio
--snippy_fbopt	string		Extra Freebayes options, eg. --theta 1E-6 --read-snp-limit 2
--snippy_opts	string		Extra options in quotes for Snippy

Used By

Subworkflows

• snippy_run - Call variants against a reference genome using Snippy.

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_RUN:
    - bactopia-variants: 1.0.4