Package: wnpp Severity: wishlist Owner: Andreas Tille <ti...@debian.org>
* Package name : pilon-non-free Version : 1.22 Upstream Author : Copyright: Copyright 2012-2017 Broad Institute, Inc. * URL : https://github.com/broadinstitute/pilon/wiki * License : GPL-2 Programming Lang: Java 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 . The code of pilon is actually free but currently there is no method to build the JAR from the scala source in Debian. This package is supposed to be replaced by a pilon package once it can be build from source (see bug #873341). Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/pilon-non-free It is planed to replace this package pilon-non-free by a pilon package once sbt will be usable again (see #873341). Unfortunately it is expected that this will take way longer than expected (see the discussion on debian-java list).
