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Table 2 Trimming statistics on demultiplexed reads from Table 1

From: GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments

Paired end reads RE # Correctly Sensitivity Triming errors
  Site trimmed   per thousand reads
GBSX GBS Y 12,381,497 99.89% 1
GBSX RAD Y 12,313,669 99.34% 7
GBSX NA N 12,364,365 99.63% 4
Stacks process_radtags Y 7,407,377 95.50% 45
Stacks process_shortreads N 7,190,394 68.29% 317
Single end reads RE # Correctly Sensitivity Triming errors
  Site trimmed   per thousand reads
GBSX GBS Y 11,878,172 95.83% 42
GBSX RAD Y 10,821,969 87.31% 127
GBSX NA N 10,835,239 87.31% 127
Stacks process_radtags Y 7,421,337 94.89% 51
Stacks process_shortreads N 7,191,440 68.29% 317
  1. The RE Site column indicates if the reads did or did not contain the ApeKI restriction enzyme sequence. Sabre does not perform read trimming and is therefor not included in this comparison.