Pilea

Pilea: profiling bacterial growth dynamics from metagenomes with sketching

Quick Start

Installation

Install Pilea in a new conda environment:

conda create -n pilea -c bioconda -c conda-forge pilea
conda activate pilea

Running Pilea

Download the example dataset from Zenodo. This dataset contains 1 million paired-end short reads from four bacterial species (Bacillus subtilis, Klebsiella pneumoniae, Morganella morganii, and Pseudomonas putida):

wget -qN --show-progress https://zenodo.org/records/15681353/files/example.tar.gz
tar -xvf example.tar.gz && cd example

Step 1: Indexing

[!TIP] If MAGs aren’t available, use pilea fetch to download a pre-built GTDB database. This reference database was constructed with pilea rebuild. If MAGs are available, they can be merged with the GTDB database via -d/--database. See pilea index -h for details.

The taxonomy mapping file (-a/--taxonomy) is optional. If provided, it needs to be a tab-separated file containing at least two columns (genome and its associated taxonomy). This file can be the output of GTDB-Tk (gtdbtk.bac120.summary.tsv) and should include only bacteria (no archaea or non-prokaryotes). MAGs must have extensions in .(fa|fna|fasta).

pilea index mags/*.fna -a gtdbtk.bac120.summary.tsv -o db

Step 2: Profiling

[!TIP] If multiple samples are available, running them in a single batch (*.fasta) helps avoid repeated database loading, which can be time-consuming if the database is large.

Both FASTA (fa|fasta) and FASTQ (fq|fastq) files are supported. By default, paired-end reads are identified with pattern _(1|2|R1|R2|fwd|rev). Use --single for single-end reads.

pilea profile *.fasta -d db -o .

PTR estimates and other metadata for MAGs that pass basic filters will be saved to output.tsv:

...  taxonomy                   coverage  dispersion  fraction  containment  PTR     log2(PTR)
...  ...Bacillus subtilis       5.9939    0.9057      1.0000    0.9936       1.5451  0.6277
...  ...Klebsiella pneumoniae   12.0417   0.9715      0.9956    0.9867       1.2804  0.3566
...  ...Morganella morganii     9.9278    0.9222      0.9716    0.9766       1.3799  0.4646
...  ...Pseudomonas_E putida_U  5.6176    0.8939      0.9955    0.9859       1.7704  0.8240

Coverage (--min-cove) represents the median per-window coverage estimated from sketched $k$ -mers (lower than per-base coverage, depending on read length and $k$ ). Dispersion (--max-disp) and fraction (--min-frac) indicate the median per-window dispersion and the fraction of covered windows, respectively. Containment (--min-cont) is the proportion of sketched $k$ -mers used for PTR estimation. See pilea profile -h for more details.

Citation

Chen, X., Xu, X., Lin, Y., Shi, X., Wang, D., & Zhang, T. (2026). Pilea: profiling bacterial growth dynamics from metagenomes with sketching. Microbiome. https://doi.org/10.1186/s40168-026-02374-0