pairplex 0.3.0

Demultiplex single-cell antibody repertoires with precision and paired insight.

PairPlex: large-scale natively paired antibody sequencing

PairPlex uses combinatorial barcoding (inspired by UDA-seq) to perform cost-effective sequencing of large numbers of natively paired antibodies by massively overloading 10x Genomics reactions.

Installation

PairPlex can be installed with pip:

pip install pairplex

Alternatively, you can install from source (which may not be entirely stable, so use at your own risk):

git clone https://github.com/brineylab/pairplex
cd pairplex
pip install .

Installation can be quickly confirmed by checking the version:

pairplex version

If the current version is displayed, installation was successful.

Usage

CLI

pairplex run /path/to/sequencing_data /path/to/output_directory

Sequencing data can be provided as a single FASTA/Q file or a directory containing one or more FASTA/Q files (optionally gzip compressed). If a directory is provided, all files in the directory will be processed (recursively).

Providing the merge_paired_reads option will instruct PairPlex to merge paired-end sequencing reads with fastp prior to processing, so the output of Illumina's bcl2fastq or Element's bases2fastq can be used directly as input:

pairplex run --merge_paired_reads /path/to/paired_reads /path/to/output_directory

By default, we assume Illumina-style naming conventions for paired-end read files. For paired FASTQ files produced by Element's bases2fastq, the platform option should be set to element.

pairplex run --merge_paired_reads --platform element /path/to/paired_reads /path/to/output_directory

[!NOTE] If the sequencing data is already merged (or wasn't paired-end to begin with), the platform option is not used, since the file naming conventions are only needed to match file pairs for read merging.

The complete list of CLI options can be displayed by running:

pairplex run --help

API

import pairplex

pairplex.run(
    sequences="/path/to/sequencing_data",
    output_directory="/path/to/output_directory",
    merge_paired_reads=True,
)

Citation

If you are using Pairplex or the dataset generated of paired antibody sequences, please cite: