| 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 |
- aPlus time to run Bowtie. We calculate Bowtie statistics separately because ALE takes Bowtie alignments as input.
- bPlus time to run BLAT.
- 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.