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 rDNA sequences curated from GenBank.

/pipelines/ \
  --sample-name test \
  --genome hg38 \
  --prealignments human_rDNA \
  --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.