#LICENSE The software was developed at the Leibniz Institute on Aging - Fritz Lipmann Institute (FLI; http://www.leibniz-fli.de/) 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 (http://genome.leibniz-fli.de/software/index.php). By downloading the package you agree with conditions of the FLI Software License Agreement for Academic Non-commercial Research (LICENSE.pdf).

KILAPE

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 (bryand@pobox.com).

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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 KILAPE.pl).

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)

3. ../KILAPE.pl

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DEPENDENCIES

REQUIRED:

Boost Libraries for C++ (www.boost.org)

Jellyfish (http://www.cbcb.umd.edu/software/jellyfish/)

BWA (http://bio-bwa.sourceforge.net/), Bowtie (http://bowtie-bio.sourceforge.net/index.shtml), or Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)

OPTIONAL (recommended):

Parallel::ForkManager perl module (http://search.cpan.org/~dlux/Parallel-ForkManager-0.7.5/ForkManager.pm)

• 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 (http://www.ebi.ac.uk/~zerbino/velvet/)

wgs-assembler (http://wgs-assembler.sourceforge.net)

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