as such required the development of novel approaches to achieve parallelization one approach to enable a modest level of parallelization of the subsequent steps is to divide the analysis by individual chromosomes 22 autosomes chromosomes 1 to 22 and two sex chromosomes chromosomes x and y however doing so results in a significant load unbalance as the size of these chromosomes varies significantly with chromosome 1 being u02dc 5 times larger than chromosome 21 see fig5 a and 5 b in addition limiting parallelization at chromosomal level restricts the use of processors to a total of 24 such that utilization of more than 24 processors cannot improve performance dependencies among these steps may be identified as a starting point for the workflow optimization the nature of ngs data generation implies that the reads can be mapped to the reference genome independently of one another the only constraint for paired end reads is that both reads in a pair should be properly oriented within proper distance table 1 summarizes these various steps and the prerequisites bwa can run in n jobs where n is the number of paired end fastq files 50 in casava 1 8 2 this is controlled by bcl conversion 39 s parameter u2014 fastq cluster count which specifies the maximum number of clusters per output fastq file it was found the default value of 4 000 000 worked reasonably well for current settings all.