debian/changelog

 unicycler (0.4.5-1) unstable; urgency=medium
 
   * Initial release (Closes: #<bug>)
+  Needs:
+    https://github.com/isovic/racon
+    https://github.com/broadinstitute/pilon/wiki
 
  -- Andreas Tille <tille@debian.org>  Fri, 25 May 2018 10:59:36 +0200

debian/control

@@ -6,7 +6,8 @@ Priority: optional
 Build-Depends: debhelper (>= 11~),
                dh-python,
                python3-all,
-               python3-setuptools
+               python3-setuptools,
+               spades
 Standards-Version: 4.1.4
 Vcs-Browser: https://salsa.debian.org/med-team/unicycler
 Vcs-Git: https://salsa.debian.org/med-team/unicycler.git
@@ -14,8 +15,12 @@ Homepage: https://github.com/rrwick/Unicycler
 
 Package: unicycler
 Architecture: any
-Depends: ${shlibs:Depends},
-         ${misc:Depends}
+Depends: ${python3:Depends},
+         ${misc:Depends},
+         spades,
+         ncbi-blast+,
+         bowtie2,
+         samtools
 Description: hybrid assembly pipeline for bacterial genomes
  Unicycler is an assembly pipeline for bacterial genomes. It can assemble
  Illumina-only read sets where it functions as a SPAdes-optimiser. It can

debian/upstream/metadata

 Reference:
-  Author: 
-  Title: 
-  Journal: 
-  Year: 
-  Volume: 
-  Number: 
-  Pages: 
-  DOI: 
-  PMID:
-  URL: 
-  eprint: 
+ - Author: Ryan R. Wick and Louise M. Judd and Claire L. Gorrie and Kathryn E. Holt
+   Title: "Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads"
+   Journal: PLOS Computational Biology
+   Year: 2017
+   Volume: 13
+   Number: 6
+   Pages: e1005595
+   DOI: 10.1371/journal.pcbi.1005595
+   PMID: 28594827
+   URL: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005595
+   eprint: http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005595&type=printable
+ - Author: Ryan R. Wick and Louise M. Judd and Claire L. Gorrie and Kathryn E. Holt
+   Title: Completing bacterial genome assemblies with multiplex MinION sequencing
+   Journal: Microbial Genomics
+   Year: 2017
+   Volume: 3
+   Number: 10
+   Pages: e000132
+   DOI: 10.1099/mgen.0.000132
+   PMID: 29177090
+   URL: http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000132
+   eprint: http://mgen.microbiologyresearch.org/deliver/fulltext/mgen/3/10/mgen000132.pdf?itemId=/content/journal/mgen/10.1099/mgen.0.000132&mimeType=pdf&isFastTrackArticle=