chain files for genomic liftover. Only used with --runMode liftOver .

VCF file with consensus SNPs (i.e. alternative allele is the major (AF>0.5) allele)

path to the directory where genome files are stored (for --runMode alignReads) or will be generated (for --runMode generateGenome)

path(s) to the fasta files with the genome sequences, separated by spaces. These files should be plain text FASTA files, they *cannot* be zipped. Required for the genome generation (--runMode genomeGenerate). Can also be used in the mapping (--runMode alignReads) to add extra (new) sequences to the genome (e.g. spike-ins).

genome files exact sizes in bytes. Typically, this should not be defined by the user.

Genome Indexing Parameters - only used with --runMode genomeGenerate

mode of shared memory usage for the genome files. Only used with --runMode alignReads.