Use prealignments with PEPPRO

One feature of the pipeline is prealignments, which siphons off reads by aligning to small genomes before the main alignment to the primary reference genome.

Ideas for common prealignment references are provided by ref_decoy.

Prealignments can be added via the command-line or included in a PEP project configuration file.

Using prealignments on the command-line

In this example, we'll align sequentially to human mitochondrial sequence (e.g. the Revised Cambridge Reference Sequence of Human Mitochondrial DNA) and then a "human_repeats" genome which is the combination of alu elements, centromeric or alpha-satellite DNA, and ribosomal sequence.

/pipelines/ \
  --sample-name test \
  --genome hg38 \
  --prealignments rCRSd human_repeats \
  --input examples/data/test_r1.fq.gz \
  --single-or-paired single \
  -O $HOME/peppro_example/

Adding prealignments to a project configuration file

See the included peppro_test.yaml for a simple example of setting prealignments in a project configuration file.