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Table 2 Performance of de-novo GBS and RAD-seq pipelines when analyzing a single FASTQ file

From: TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data

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
  1. The FASTQ file analyzed is the same as that used to produce TableĀ 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