Table 2.

Performance of de-novo GBS and RAD-seq pipelines when analyzing a single FASTQ file

Software	Size of intermediate files generated (Gb)	RAM utilized by pipeline (Gb)	Total time, across all processor cores, to process 203,000,000 FASTQ reads and output genotypes (min)
UNEAK pipeline in TASSEL 3.0	0.5	1.9	22
Stacks 1.4	8.2	4.2	424
pyRAD 3.0	40.9	18.5	23,215

The FASTQ file analyzed is the same as that used to produce Table 1. pyRAD differs from UNEAK and Stacks in that it searches for insertions and deletions, whereas the other two only search for substitutions, which is likely to account to for the substantially longer processing time