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
JF  - 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
U6  - https://doi.org/10.1093/gigascience/giy029
SN  - 2047-217X
VL  - 7
IS  - 5
SP  - 1
EP  - 6
PB  - Oxford University Press
CY  - Oxford
ER  - 
TY  - GEN
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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 477 
KW  - genome assembly
KW  - mate-pairs
KW  - in silico
KW  - scaffolding
KW  - shotgun sequencing
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-419225
ER  - 
TY  - JOUR
A1  - Hofreiter, Michael
A1  - Hartmann, Stefanie
T1  - Reconstructing protein-coding sequences from ancient DNA
JF  - Odorant binding and chemosensory proteins
N2  - Obtaining information about functional details of proteins of extinct species is of critical importance for a better understanding of the real-life appearance, behavior and ecology of these lost entries in the book of life. In this chapter, we discuss the possibilities to retrieve the necessary DNA sequence information from paleogenomic data obtained from fossil specimens, which can then be used to express and subsequently analyze the protein of interest. We discuss the problems specific to ancient DNA, including mis-coding lesions, short read length and incomplete paleogenome assemblies. Finally, we discuss an alternative, but currently rarely used approach, direct PCR amplification, which is especially useful for comparatively short proteins.
KW  - re-sequencing
KW  - mapping
KW  - genome assembly
KW  - targeted assembly
KW  - SRAssembler
KW  - ancient DNA
KW  - reference sequence
KW  - paleogenomics
Y1  - 2020
SN  - 978-0-12-821157-1
U6  - https://doi.org/10.1016/bs.mie.2020.05.008
SN  - 0076-6879
VL  - 642
SP  - 21
EP  - 33
PB  - Academic Press,  an imprint of Elsevier
CY  - Cambridge, MA.
ER  -