Specify additional "genomes" of spike-in controls for downstream calculation of bisulfite conversion efficiency

[pdemko]

Description of feature

Library preparation kits come with unmethylated and methylated DNA controls that are added to samples (e.g. NEBNext EM-seq). It would be useful to supply methylseq with the fasta sequences of the controls and have it perform additional alignment, deduplication, and extraction using those references. This would help enable calculation of bisulfite/enzymatic conversion efficiency.

Thank you for providing this excellent pipeline!

[cjfields]

At the moment, we're basically including them as part of the main reference genome FASTA and analyzing outside of methylseq. Having a way to include them separately would also be useful so additional spike-in specific analyses could be performed.