Package: pilon
Version: 1.24-4build1
Architecture: all
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 613
Depends: default-jre, java-wrappers, libhtsjdk-java, libcommons-lang-java, scala-library
Conflicts: pilon-non-free
Replaces: pilon-non-free
Section: science
Priority: optional
Homepage: https://github.com/broadinstitute/pilon/wiki
Description: automated genome assembly improvement and variant detection tool
 Pilon is a software tool which can be used to:
  * Automatically improve draft assemblies
  * Find variation among strains, including large event detection
 Pilon requires as input a FASTA file of the genome along with one or more
 BAM files of reads aligned to the input FASTA file. Pilon uses read
 alignment analysis to identify inconsistencies between the input genome and
 the evidence in the reads. It then attempts to make improvements to the
 input genome, including:
  * Single base differences
  * Small indels
  * Larger indel or block substitution events
  * Gap filling
  * Identification of local misassemblies, including optional opening
    of new gaps
