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Table 2 Wall-clock runtimes (in hours, minutes and seconds) and memory usage (as measured by the maximum resident set size, in gigabytes) for several assembly evaluation tools

From: Evaluation of de novo transcriptome assemblies from RNA-Seq data

  Assembly T Assembly O Assembly S
Program Runtime Memory Runtime Memory Runtime Memory
RSEM-EVAL a 1 h 4 m 57 s 2.02 GB 4 h 40 m 36 s 8.18 GB 34 m 57 s 1.23 GB
Genovo 6 d 11 h 54 m 3 s 192.23 GB >1 week 4 d 15 h 3 m 3 s 188.79 GB
ALE a 12 h 39 m 36 s 0.67 GB 6 d 23 h 23 m 13 s 2.31 GB 7 h 33 m 1 s 0.59 GB
REF-EVAL, contig b 3 s 0.19 GB 8 s 0.33 GB 2 s 0.2 GB
REF-EVAL, nucleotide b 8 s 0.39 GB 33 s 1.27 GB 6 s 0.33 GB
REF-EVAL, KC score 1 m 18 s 2.09 GB 1 m 30 s 2.37 GB 1 m 13 s 2.03 GB
Bowtie 15 m 42 s 0.11 GB 1 h 1 m 38 s 0.31 GB 11 m 16 s 0.1 GB
BLAT 35 m 14 s 0.0 GB 1 h 51 m 1 s 0.01 GB 28 m 19 s 0.0 GB
  1. aPlus time to run Bowtie. We calculate Bowtie statistics separately because ALE takes Bowtie alignments as input.
  2. bPlus time to run BLAT.
  3. Each tool was run on three different assemblies of the real mouse data. Assembly T was produced by Trinity with its default parameters (52,667 contigs, 33 million nucleotides). Assembly O was produced by Oases with its default parameters (160,455 contigs, 115 million nucleotides). Assembly S was produced by SOAPdenovo-Trans with its default parameters (79,460 contigs, 28 million nucleotides). Multithreaded programs (RSEM-EVAL, REF-EVAL and Bowtie) were run with 16 threads. All programs were run on a compute server with an Intel®; Xeon®; CPU E5-2660 v2 2.20 GHz processor and 500 gigabytes RAM. Genovo had not finished running on assembly O after more than 1 week. KC score, k-mer compression score.