sylph_profile

Tags: metagenomics profiling taxonomy abundance ani sylph sample-scope

Profile metagenome samples against a database using Sylph.

Uses Sylph to profile metagenomic samples for taxonomic abundance and containment ANI against a provided database. It is designed to be extremely fast and memory-efficient.

Uses explicit positional record fields for reads:

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

Inputs

record (
    meta: Record,
    r1: Path?,
    r2: Path?,
    se: Path?,
    lr: 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
lr	Path?	Long reads (ONT/PacBio)

db: Path

Name	Type	Description
db	Path	Path to the Sylph database file (*.syldb)

Outputs

record (
    meta: Record,
    tsv: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	TSV file with profiling results
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

Sylph Profile Parameters

Parameter	Type	Default	Description
--sylph_db	string		The path to a sylph formatted database
--sylph_k	integer	31	K-mer size for sketching
--sylph_min_spacing	integer	30	Minimum spacing between selected k-mers on the database genomes
--sylph_subsample_rate	integer	200	Subsample rate for sketching
--sylph_min_ani	integer	95	Minimum adjusted ANI to consider. Smaller than 95 for profile will give inaccurate results.
--sylph_min_kmers	integer	50	Exclude genomes with less than this number of sampled k-mers
--sylph_min_correct	integer	3	Minimum k-mer multiplicity needed for coverage correction. Higher values gives more precision but lower sensitivity
--sylph_estimate_unknown	boolean	false	Estimate true coverage and scale sequence abundance in profile by estimated unknown sequence percentage
--sylph_opts	string		Extra options in quotes for Sylph

Used By

Subworkflows

• sylph - Profile microbial composition using Sylph.

Workflows

• sylph - Taxonomic profiling by abundance-corrected MinHash.

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)

• Sylph
  Shaw J, and Yu YW Rapid species-level metagenome profiling and containment estimation with sylph. Nature Biotechnology (2024)

Source

View source on GitHub

Version

SYLPH_PROFILE:
    - sylph: 0.9.0