rduckhts_fastq_multi: Read multiple FASTQ files into a DuckDB table

In Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

Read multiple FASTQ files into a DuckDB table

Description

Read and combine multiple FASTQ files via UNION ALL BY NAME, materialising the result as a DuckDB table. Each row includes a filename column identifying its source file.

Usage

rduckhts_fastq_multi(
  con,
  table_name,
  files,
  mate_path = NULL,
  interleaved = FALSE,
  sequence_encoding = NULL,
  quality_representation = NULL,
  input_quality_encoding = NULL,
  scan_mode = NULL,
  .params = NULL,
  overwrite = FALSE
)

Arguments

con	A DBI connection to DuckDB with the duckhts extension loaded.
table_name	Name of the DuckDB table to create.
files	Character vector of file paths or glob patterns.
mate_path	Optional mate file path (for paired-end).
interleaved	Logical; TRUE if file contains interleaved paired reads.
sequence_encoding	Optional sequence encoding.
quality_representation	Optional quality representation.
input_quality_encoding	Optional input quality encoding override.
scan_mode	Optional scan mode ("auto" or "sequential").
.params	Optional data.frame with per-file parameter overrides.
overwrite	Logical; if TRUE, replace an existing table.

Value

Invisible TRUE on success.

Rduckhts documentation built on Oct. 25, 2026, 1:08 a.m.