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.

Using prealignments with looper

To change the prealignments, you just need to add a prealignment sample attribute with a space-separated list of all genomes you want to prealign to.

For example, adding this to your PEP project config yaml file will instruct the pipeline to pre-align to human_rDNA, then rCRSd, before doing the primary alignment to hg38:

    - if: 
        organism: ["human", "Homo sapiens", "Human", "Homo_sapiens"]
        prealignments: human_rDNA rCRSd

You could accomplish the same thing in a less elegant way by adding these columns to your sample table so it looks something like this:

sample_name genome prealignments other columns...
sample1 hg38 human_rDNA rCRSd ...
sample2 hg38 human_rDNA rCRSd ...
sample3 hg38 human_rDNA rCRSd ...

Using prealignments on the command-line

If you want to adjust this for a single sample run, you just pass the values on the command line:

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