baqlava

Bacteriophage and vIral Analysis of Large-scale metAgenomic data

What is baqlava?

baqlava (Bacteriophage and vIral Analysis of Large-scale metAgenomic data) is a computational pipeline for identifying and profiling viruses — particularly bacteriophages — from shotgun metagenomic data. It uses a database of viral marker genes to accurately detect and quantify viral populations in complex microbial communities.

baqlava answers the question: “Which viruses (especially bacteriophages) are present in this metagenome, and at what abundance?”

📄 GitHub
📖 Documentation

When to Use baqlava

Use baqlava when you want to:

Profile the virome (viral community) from metagenomic data
Detect bacteriophages alongside bacteria in the same dataset
Study phage-bacteria interaction dynamics
Integrate viral profiling with HUMAnN/MetaPhlAn results

Note

baqlava is complementary to MetaPhlAn. While MetaPhlAn focuses on bacteria, archaea, and microbial eukaryotes, baqlava targets viruses and phages.

Installation

Via conda

conda create -n baqlava -c biobakery baqlava
conda activate baqlava

Via pip

pip install baqlava

Database setup

# Download viral marker database
baqlava_databases --download all /path/to/databases/

Basic Usage

baqlava \
  --input sample.fastq.gz \
  --output output_directory/ \
  --threads 8

Key options

Option	Description
`--input`	Input FASTQ file(s)
`--output`	Output directory
`--threads`	Number of CPU threads
`--bypass-host-removal`	Skip host read removal (if already done)

Output Files

File	Contents
`*_viral_abundance.tsv`	Viral species/family abundances (RPK)
`*_viral_profile.tsv`	Presence/absence profile of viral taxa

Integration with MetaPhlAn

baqlava was designed to complement MetaPhlAn. When using MetaPhlAn with the --add_viruses flag, a subset of viruses can be profiled. baqlava provides more comprehensive viral profiling:

# MetaPhlAn with basic viral support
metaphlan sample.fastq.gz \
  --add_viruses \
  --input_type fastq \
  -o sample_profile.txt

# baqlava for comprehensive viral profiling
baqlava \
  --input sample.fastq.gz \
  --output baqlava_output/

Tips & Gotchas

Tip

Host removal first — Remove human (or other host) reads before running baqlava. Use KneadData for this.

Warning

Virome enrichment vs. total metagenomics — baqlava works on standard shotgun metagenomics, but viral sequences are often at low abundance. Virome-enriched protocols (e.g., VLP extraction) will give better sensitivity.

Tip

Combine with MetaPhlAn results — Join baqlava viral abundances with MetaPhlAn bacterial abundances for a comprehensive community profile.

--- title: "baqlava" subtitle: "Bacteriophage and vIral Analysis of Large-scale metAgenomic data" --- ## What is baqlava? **baqlava** (Bacteriophage and vIral Analysis of Large-scale metAgenomic data) is a computational pipeline for identifying and profiling viruses — particularly bacteriophages — from shotgun metagenomic data. It uses a database of viral marker genes to accurately detect and quantify viral populations in complex microbial communities. baqlava answers the question: **"Which viruses (especially bacteriophages) are present in this metagenome, and at what abundance?"** - 📄 [GitHub](https://github.com/biobakery/baqlava) - 📖 [Documentation](https://github.com/biobakery/baqlava/wiki) --- ## When to Use baqlava Use baqlava when you want to: - Profile the virome (viral community) from metagenomic data - Detect bacteriophages alongside bacteria in the same dataset - Study phage-bacteria interaction dynamics - Integrate viral profiling with HUMAnN/MetaPhlAn results ::: {.callout-note} baqlava is complementary to MetaPhlAn. While MetaPhlAn focuses on bacteria, archaea, and microbial eukaryotes, baqlava targets viruses and phages. ::: --- ## Installation ### Via conda ```bash conda create -n baqlava -c biobakery baqlava conda activate baqlava ``` ### Via pip ```bash pip install baqlava ``` ### Database setup ```bash # Download viral marker database baqlava_databases --download all /path/to/databases/ ``` --- ## Basic Usage ```bash baqlava \ --input sample.fastq.gz \ --output output_directory/ \ --threads 8 ``` ### Key options | Option | Description | |--------|-------------| | `--input` | Input FASTQ file(s) | | `--output` | Output directory | | `--threads` | Number of CPU threads | | `--bypass-host-removal` | Skip host read removal (if already done) | --- ## Output Files | File | Contents | |------|----------| | `*_viral_abundance.tsv` | Viral species/family abundances (RPK) | | `*_viral_profile.tsv` | Presence/absence profile of viral taxa | --- ## Integration with MetaPhlAn baqlava was designed to complement MetaPhlAn. When using MetaPhlAn with the `--add_viruses` flag, a subset of viruses can be profiled. baqlava provides more comprehensive viral profiling: ```bash # MetaPhlAn with basic viral support metaphlan sample.fastq.gz \ --add_viruses \ --input_type fastq \ -o sample_profile.txt # baqlava for comprehensive viral profiling baqlava \ --input sample.fastq.gz \ --output baqlava_output/ ``` --- ## Tips & Gotchas ::: {.callout-tip} **Host removal first** — Remove human (or other host) reads before running baqlava. Use KneadData for this. ::: ::: {.callout-warning} **Virome enrichment vs. total metagenomics** — baqlava works on standard shotgun metagenomics, but viral sequences are often at low abundance. Virome-enriched protocols (e.g., VLP extraction) will give better sensitivity. ::: ::: {.callout-tip} **Combine with MetaPhlAn results** — Join baqlava viral abundances with MetaPhlAn bacterial abundances for a comprehensive community profile. ::: --- ## Further Reading - [baqlava GitHub](https://github.com/biobakery/baqlava) - [Biobakery tools overview](https://huttenhower.sph.harvard.edu/tools/)