precellar.utils.multiplex_fastq#

precellar.utils.multiplex_fastq(input_read1, output_read1, output_barcode, *, input_read2=None, output_read2=None, compression=None, compression_level=None, num_threads=16)#

Create multiplexed FASTQ files by merging multiple FASTQ files into single output files, while generating barcodes for each read based on their file of origin.

This function is useful for methods such as SMART-seq.

Parameters:

  • input_read1 (list[str]) – List of paths to the first read (R1) FASTQ files.

  • output_read1 (str) – Path to the output file for merged R1 reads.

  • output_barcode (str) – Path to the output barcode file.

  • input_read2 (list[str] | None) – Optional list of paths to the second read (R2) FASTQ files.

  • output_read2 (str | None) – Optional path to the output file for merged R2 reads.

  • compression (Literal['gzip', 'zst'] | None) – Compression algorithm to use. If None, the compression algorithm will be inferred from the file extension.

  • compression_level (int | None) – Compression level to use.

  • num_threads (int) – Number of threads to use for compression.

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