Out of Scope

Out of scope #

Things mbf-fastq-processor will explicitly not do and that won’t be implemented.

Anything based on averaging phred scores #

Based on the average quality in a sliding window. Arithmetic averaging of phred scores is wrong.

see ExtractMeanQuality

Corresponding options in other software #

  • Trimmomatic SLIDINGWINDOW
  • fastp –cut_front
  • fastp –cut_tail
  • fastp –cut_right

Fast5 #

https://medium.com/@shiansu/a-look-at-the-nanopore-fast5-format-f711999e2ff6 Oxford Nanopore squiggle data. Apparently no formal spec.

kallisto BUS format #

- a brief barcode/umi format for single cell RNA-seq
- needs an 'equivalance class' - i.e. at least pseudo alignment
- weird length restrictions on barcodes and umis (1(!)-32), 
  but stores the length in an uint32...

Alignment #

While it’s tempting to leverage the fastq parsing for an aligner, aligning molecules to references is out of scope for the 1.0 target.