AGapEs – Gap filling based on Template Sequence for aDNA data

AGapEs

:: DESCRIPTION

AGapEs (ancestral gap estimation) is an optimization-based mathod to fill in inter-contig gaps using a combination of a template obtained from related extant genomes and aDNA reads.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

AGapEs

:: MORE INFORMATION

Citation

Luhmann N, Doerr D, Chauve C.
Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes.
Microb Genom. 2017 Jul 8;3(9):e000123. doi: 10.1099/mgen.0.000123. PMID: 29114402; PMCID: PMC5643016.

Scaffold-filling – Software for Filling the Scaffold

Scaffold-filling

:: DESCRIPTION

Scaffold-filling inserts genes from a fully sequenced genome into predicted positions within the gaps of a genome with a lower quality assembly.

::DEVELOPER

Sankoff Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

Scaffold-filling

:: MORE INFORMATION

Citaion

Scaffold filling, contig fusion and comparative gene order inference.
Muñoz A, Zheng C, Zhu Q, Albert VA, Rounsley S, Sankoff D.
BMC Bioinformatics. 2010 Jun 4;11:304.