fermi2 can assemble reads into unitigs. Unitig output can be further analysed by alignment to a reference genome using bwa-mem, and based on the alignment variants can be called using the fermi-variants tool.

Usage:   fermi2.pl unitig [options] <in.fq>

Options: -p STR    output prefix [fmdef]
         -s STR    approximate genome size [100m]
         -2        2-pass error correction
         -l INT    primary read length [101]
         -T INT    use INT-mer for post-trimming/filtering [61]
         -k INT    min overlap length during unitig construction [based on -l]
         -o INT    min overlap length during graph cleaning [based on -l]
         -m INT    min overlap length for unambiguous merging [based on -l]
         -t INT    number of threads [4]
         -E        don't apply error correction