merge develop/select references

Goals:

• Update reference-selection with nextflow pipeline
• Re-implement reference-selection according to the notes
• Test for reference selection accuracy

Files:

• A new script, pipeline/ref-selection.nf, was created for the pipeline.
• Jackie provided two scripts, one for filtering the references and one for choosing the best references.
  • scripts/filter_refs.sh - This file performs kmer-mask filtering of references.
  • scripts/map_refs.sh - This file scores the filtered references and creates a list of possible candidate genomes.

Testing:

Testing conducted to check accuracy of references chosen with sample reads and a known reference genome.

• Downsampling - Tested with shakya reference genome at 25%, 50% and 75% of total reads.
• Permutation - Tested with shakya reference genome.

TODO's:

• Currently the filtering step is optional. Need to remove mapping step dependency of filtering step.