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#LICENSE The software was developed at the Leibniz Institute on Aging - Fritz Lipmann Institute (FLI; under a mixed licensing model. Researchers at academic and non-profit organizations can use KILAPE using the included license, while for-profit organizations are required to purchase a license ( By downloading the package you agree with conditions of the FLI Software License Agreement for Academic Non-commercial Research (LICENSE.pdf).


K-masking and Iterative Local Assembly of Paired Ends

KILAPE (K-masking and Iterative Local Assembly of Paired Ends) is an automated scaffolding and gap filling software pipeline which predicts repetitive elements in Next Generation Sequencing read libraries without resorting to a reference sequence. The package of KILAPE consists of pre-compiled C++ program modules as well as a set of Perl scripts for data preparation and for processing within the pipeline itself.

KILAPE performs scaffolding and local assemblies in an iterative manner as defined in a configuration file (see "demo" directory for a template file). Scaffolds are constructed based on libraries defined by a SCAFFOLD parameter, and local assembly/gap filling using LA_VELVET/LA_CELERA parameters. If a local assembly is performed, then read pairs (for one or more libraries) in which at least one read map unambiguously to a putative scaffold are segregated into a separate directory, and then a velvet assembly is performed.

Questions and bug reports should be addressed to the software developer Bryan Downie (


INSTALLATION: Extract the downloaded archive to a local directory. Currently, KILAPE binaries have been compiled for standard 64-bit Linux distributions.

  1. tar xzf kilape_v1.0b.tar.gz

  2. Copy files to installation directory. Be sure to maintain directory structure (i.e. "bin" directory containing binaries in the directory containing

A sample configuration file along with explanations can be found in the "demo" directory.

To test your installation:

  1. cd demo

  2. Edit kilape.conf to account for binary locations (e.g. path to bowtie2)

  • scaffolds.demo.fasta should be similar/identical to scaffolds.velvet.fasta (depending on velvet version)
  1. ../




Boost Libraries for C++ (

Jellyfish (

BWA (, Bowtie (, or Bowtie2 (

OPTIONAL (recommended):

Parallel::ForkManager perl module (

  • Without this, perl scripts will need to be altered and local assembly will not be run in parallel.
  • Also, mapping of read libraries will not be performed in parallel.

velvet (

wgs-assembler (

  • Required for local assembly functionality
  • Local assembly function is currently in beta and not supported.


K-masking and Iterative Local Assembly of Paired Ends. \nFree for academic and non-profit use. By downloading you agree with the LICENSE included in the pa.






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