Paket: pilon (1.24-4)

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Homepage [github.com]

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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dep: default-jre

Standard Java or Java compatible Runtime
dep: java-wrappers

wrappers for java executables
dep: libcommons-lang-java

Commons Lang - an extension of the java.lang package
dep: libhtsjdk-java

Java API for high-throughput sequencing data (HTS) formats
dep: scala-library

Scala standard library

pilon herunterladen

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