Check Requirements for Long-Read Processing

Source: R/validate.R

Verifies that all tools and packages needed for processing raw long-read FASTQ files are available.

require_long_read_processing()

Value

Invisible TRUE if all requirements are met

Details

Processing raw long-read data (FLNC FASTQ) requires:

  • minimap2: For spliced alignment of long reads

  • samtools: For BAM file processing

  • bambu (Bioconductor): For long-read transcript quantification

Installation

For external tools:

# minimap2 (https://github.com/lh3/minimap2)
conda install -c bioconda minimap2

# samtools (https://www.htslib.org/)
conda install -c bioconda samtools

For R packages:

BiocManager::install("bambu")

Examples

if (FALSE) { # \dontrun{
# Check before processing long-read FASTQ
require_long_read_processing()
} # }