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Source: pilon
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 11~),
javahelper,
scala,
libhtsjdk-java
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/pilon
Vcs-Git: https://salsa.debian.org/med-team/pilon.git
Homepage: https://github.com/broadinstitute/pilon/wiki
Package: pilon
Architecture: all
Depends: ${misc:Depends},
default-jre | java-runtime,
java-wrappers,
libhtsjdk-java,
libcommons-lang-java,
scala-library
Conflicts: pilon-non-free
Replaces: pilon-non-free
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
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