alternative way of mapping reads to host vs parasite genome

[bguo068]

Currently, we first map all reads to the human genome, and then any unmap reads are mapped to the parasite genome. This strategy aggressively removes reads that could map to both the human and parasite genomes.

An alternative way is to combine the human and parasite genomes, map reads to the pseudo, combined genome, and keep alignment related to the parasite chromosomes.

[bguo068]

• make merged genome and their associated index files
• Remove processes
  - [ ] BOWTIE2_ALIGN_TO_HOST
  - [ ] SAMTOOLS_VIEW_RM_HOST_READS
  - [ ] SAMTOOLS_FASTQ
  - [ ] BOWTIE2_ALIGN_TO_PARASITE)
• Add new process:
  • BOWITE2_ALIGN_TO_COMBINED_GENOME
  • SAMTOOLS_VIEW_KEEP_PARASITE_CHROMOSOMES
• Add a parameter to allows to choose one of the possible mapping strategy, either
  • map to human genome and then map unmapped reads to parasite genome
  • map to combined genome and extract reads mapped to parasite genome