TY  - JOUR
A1  - Grau, José Horacio
A1  - Hackl, Thomas
A1  - Koepfli, Klaus-Peter
A1  - Hofreiter, Michael
T1  - Improving draft genome contiguity with reference-derived in silico mate-pair libraries
T2  - GigaScience
N2  - Background

Contiguous genome assemblies are a highly valued biological resource because of the higher number of completely annotated genes and genomic elements that are usable compared to fragmented draft genomes. Nonetheless, contiguity is difficult to obtain if only low coverage data and/or only distantly related reference genome assemblies are available.

Findings

In order to improve genome contiguity, we have developed Cross-Species Scaffolding—a new pipeline that imports long-range distance information directly into the de novo assembly process by constructing mate-pair libraries in silico.

Conclusions

We show how genome assembly metrics and gene prediction dramatically improve with our pipeline by assembling two primate genomes solely based on ∼30x coverage of shotgun sequencing data.
KW  - genome assembly
KW  - mate-pairs
KW  - in silico
KW  - scaffolding
KW  - shotgun sequencing
Y1  - 2018
UR  - https://publishup.uni-potsdam.de/frontdoor/index/index/docId/41921
SN  - 2047-217X
VL  - 7
IS  - 5
SP  - 1
EP  - 6
PB  - Oxford University Press
CY  - Oxford
ER  -