Package: pilon (1.24-2)

[ Source: pilon  ]

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

Other Packages Related to pilon

• 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

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