machine spec.
Intel(R) Xeon(R) 2CPU 3GHz Linux Red Hat 3.4.6-8 x86_64 2CPU/ 8GB memory
Intel(R) Xeon(R) 2CPU 3GHz Linux Red Hat 3.4.6-8 x86_64 2CPU/ 8GB memory
Alignment Tools
| Name | Version | Information | Comments | |
| TM1 | blat | v.34 | http://genome.ucsc.edu/cgi-bin/hgBlat | |
| TM2 | MAQ | v.0.7.1 | http://maq.sourceforge.net/ | |
| TM3 | bwa | v.0.4.9 | http://maq.sourceforge.net/bwa-man.shtml | |
| TM4 | ssaha2 | v.2.3.0.1 | http://www.sanger.ac.uk/Software/analysis/SSAHA2/ |
Assembly Tools
| Name | Version | Information | Comments | |
| TA1 | velvet | v.34 | http://www.ebi.ac.uk/~zerbino/velvet/ | |
| TA2 | EDENA | v.0.7.1 | ||
| TA3 | allpaths | v.0.4.9 |
Evaluation Data
| Evaluation Data | Targeted Genome | Sequencing instruments | Reference | Raw Data
(Short Read Archives) |
Projects | ||
| E1 | bacteria | Pseudomonas syringae pv.syringae B728a | Pseudomonas syringae pv.syringae B728a (Feil et al., 2005) (Refseq: NC_007005) 6 094 698 bp |
illumina/Solexa | Farrer et al., “‘De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads.” FEMS Microbiol Lett. 2009 Feb;291(1):103-11, |
European Nucleotide Archive: project ID:32555 | — |
| E2 | plant | Arabidopsis thaliana Col-0 | Arabidopsis thaliana Col-0 (1001 genomes) | illumina/Solexa | Ossowski et al., “Sequencing of natural strains of Arabidopsis thaliana with short reads”, Genome Res. 2008 Dec;18(12):2024-33., PMID: 18818371 |
SRX000702 | http://1001genomes.org |
Evaluation Data
| Data Name | Size of targeted Genome | Original number of short reads | The number of quality filtered reads | mapped number | process time | options | ||
| E1_1 | B728a | 6 094 698 bp | 3 551 133 paired reads | 3 535 967 paired reads | ||||
| E1_2 | 7 102 266 unpaired reads |
7 071 934 unpaired reads |
(ssaha2) (blat) (MAQ) (BWA2) |
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| A2 | ||||||||
| A3 |
Evaluation Data
| tool | options | process time | ||
| E1_2? | blat | -out=blast8 | real 5m16.141s user 5m12.198s sys 0m1.952s |
|