demux_qc

Synopsis

singularity run [run options...] --app demux_qc <container> [app options...]

Description

Compute quality control checks on demultiplexed data. Prints the total number of sequencing reads and how many were of undetermined indices, meaning that they contained indices that were not present in the sample file. Additionally prints how many of the undetermined index reads belong to possible primer pairs, i.e., they are likely due to errors in the provided sample list and not just faulty reads from the sequencer.

Options

# Required
-p    The sequencing platform used. Can either be 'nextseq' or 'miseq'.

# Optional
-h    Print the help page.

Examples

singularity run \
  -B base_resources:/opt/resources \
  -B downloaded:/opt/analysis \
  --app demux_qc miptools.sif -p 'nextseq'

singularity run \
  -B base_resources:/opt/resources \
  -B downloaded:/opt/analysis \
  --app demux_qc miptools.sif -p 'miseq'