Quickstart¶

Basic usage¶

lbqc -i <fastq_pass_dir> -o <output_dir> -b <barcodes>

Using a built-in barcode preset¶

Three barcode libraries are included. Pass the preset keyword to -b:

Keyword	Description
EV	Expression Vector — 3 sites x 256 barcodes (768 total)
AP	Assembly Plasmid — 3 sites x 256 barcodes (768 total)
TS	TritSeq — 4 sites x 4 positions x 3 barcodes (48 total)

lbqc -i fastq_pass/ -o results/ -b EV

Using a custom barcode file¶

Provide a path to a FASTA file where each entry is one barcode sequence and all headers are unique:

lbqc -i fastq_pass/ -o results/ -b /path/to/barcodes.fa

Trimming adapters¶

Nanopore reads carry the ONT Rapid (RAP) adapter behind an inconsistently basecalled leader sequence, adding roughly 90 bp of non-biological sequence to the front of most reads. Use -T to remove the adapter and its leader with cutadapt before alignment:

lbqc -i fastq_pass/ -o results/ -b EV -T

A <name>.cutadapt.txt report is written to the output directory, and the trimming stats are printed to the console.

Full example¶

lbqc \
  -i /data/run01/fastq_pass/ \
  -o /results/run01_EV/ \
  -b EV \
  -r enzymes.txt \
  -T \
  -S

See the CLI Reference for all available options.