Evaluating Genome Assembly Accuracy

REAPR v1.0.18^{38 (link)} (utilizing SMALT v0.7.0.1⁹⁷) was used with the Illumina Nextera mate-pair (6 kbp) and Illumina PE (600 bp) libraries to evaluate the correctness of assemblies and QUAST v4.1^{90 (link)} was applied for contiguity and gene prediction statistics. Completeness of the assemblies was assessed using CEGMA v2.5^{35 (link)} (utilizing GeneWise v2.4.1^{98 (link)}, HMMER v3.0^{99 (link)} and NCBI BLAST + v2.2.29 + ^{93 (link)}) with parameter optimization for vertebrate genomes (–vrt) and BUSCO v3.0.2^{34 (link)} (utilizing NCBI BLAST + v2.2.29 + , HMMER v3.1^{99 (link)} and AUGUSTUS v3.2.1^{100 (link)}).

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Fischer C., Koblmüller S., Börger C., Michelitsch G., Trajanoski S., Schlötterer C., Guelly C., Thallinger G.G, & Sturmbauer C. (2021). Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika. Scientific Reports, 11, 4309.

Publication 2021

Nextera mate-pair

Blast 2 Gene Genomes Vertebrate

Corresponding Organization : University of Graz

Other organizations : Medical University of Graz

Top 5 similar protocols

Variable analysis

independent variables

REAPR v1.0.18
SMALT v0.7.0.1
Illumina Nextera mate-pair (6 kbp) library
Illumina PE (600 bp) library
QUAST v4.1
CEGMA v2.5
GeneWise v2.4.1
HMMER v3.0
NCBI BLAST + v2.2.29 +
BUSCO v3.0.2
HMMER v3.1
AUGUSTUS v3.2.1

dependent variables

Correctness of assemblies
Contiguity and gene prediction statistics
Completeness of the assemblies

control variables

Parameter optimization for vertebrate genomes (–vrt)

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