Assemble reads using the Unicycler assembler.
This is a KBase wrapper for Unicycler, an assembly pipeline for bacterial genomes. Unicycler can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible assemblies, give it both Illumina reads and long reads, and it will conduct a hybrid assembly.
More details on Unicycler can be found in publication [1] at the bottom of this App detail page, and details of how it is used to assemble bacterial genomes can be found in publication [2].
Related Publications
- [1] Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017. doi: 10.1371/journal.pcbi.1005595 , http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005595
- [2] Wick RR, Judd LM, Gorrie CL, Holt KE. Completing bacterial genome assemblies with multiplex MinION sequencing. Microb Genom 2017. doi: 10.1099/mgen.0.000132 , https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000132
App Specification:
https://github.com/jmchandonia/kb_unicycler/tree/0a192937c92f1e6920306bb4d1bd437ced9f55c0/ui/narrative/methods/run_unicyclerModule Commit: 0a192937c92f1e6920306bb4d1bd437ced9f55c0