ska fasta <input fasta file>

ska fastq <input fastq file 1> <input fastq file 2>

ska merge <list of skf files to merge>

ska align merged.skf

SKA map -r <reference fasta file> merged.skf

Timings were done using the duration function using high resolution clock time points from the c++ chrono library. This timing is reported by SKA for many of the functions it performs.

Memory usage was calculated using valgrind massif with the following commands for each analysis run:

valgrind --tool=massif --pages-as-heap=yes --massif-out-file=m.out <command>
grep mem_heap_B m.out | sed -e 's/mem_heap_B=\(.*\)/\1/' | sort -g | tail -n 1