A method to improve mappings on circular genomes, using the BWA mapper.
meta
Groovy Map containing reference information e.g. [ id:'sample1' ]
[ id:'sample1' ]
reference
Genome fasta file
*.fasta
meta2
elongation_factor
The number of bases that the ends of the target chromosome in the reference genome should be elongated by
meta3
target
The name of the chromosome in the reference genome that should be elongated
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
versions
File containing software versions
versions.yml
fasta
elongated
File listing the chromosomes that were elongated
*_elongated
Creating a modified reference genome, with an elongation of the an specified amount of bases