Download the binary file to a directory in your path. Make sure the binary file has execute permission (chmod +x) and its directory is in your PATH variable (or define a shell alias 'urmap' with the full path name).
Use the make_ufi command to create an index for the reference genome. Input is FASTA. Currently, urmap is not alt-aware and I therefore recommend that alt chromosomes should be removed from the human reference.
urmap -make_ufi hg38.fa -output hg38.ufi
urmap -map2 sample_R1.fastq.gz -reverse sample_R2.fastq.gz
-ufi hg38.ufi -samout sample.sam
Use the map command to map unpaired reads.
urmap -map sample.fastq.gz -ufi hg38.ufi -samout sample.sam