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Unicycler v0.5.0

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@rrwick rrwick released this 23 Jan 02:27
· 3 commits to main since this release
v0.5.0
ffefbf8

This release contains the most changes in a while! They include:

  • Fixed compatibility with modern versions of SPAdes.
    • Unicycler now works with SPAdes v3.15.3 (current at the time of writing).
    • Starting with version v3.13.1, SPAdes stopped saving graph files for each k-mer size (read more here). Since Unicycler depends on having a graph for each k-mer size, it was necessary to change how Unicycler run SPAdes.
    • Addresses #218, #225, #244, #251, #269, #275.
  • Removed Pilon polishing at the end of Unicycler's pipeline.
    • I have learned a lot about polishing in recent years (see the Polypolish paper), and have decided that it's best to leave this out of Unicycler. I.e. if you want to polish your assemblies, that will need to be done in a separate post-Unicycler step.
    • Pilon, Samtools and Bowtie2 are no longer dependencies of Unicycler.
    • Addresses #198, #212, #216, #246, #262, #265, #280, #283.
  • Removed read correction at the start of Unicycler's pipeline.
    • I have found that read correction isn't usually necessary or helpful, so I was in the habit of using the --no_correct option in previous versions of Unicycler to turn this off. That option no longer exists, as read correction isn't available in Unicycler anymore.
    • I still recommend that you do some read QC before assembly (fastp is one of my favourite tools for this).
    • Addresses #208, #214.
  • Unicycler now saves raw SPAdes graphs for each k-mer size with the default --keep level.
    • This is because I often found it useful to look at lower-k-mer graphs when investigating tricky parts of genomes.
  • Removed some old and/or experimental components:
    • unicycler_align command
    • unicycler_check command
    • unicycler_polish command (#202, #226, #228, #229, #239)
    • unicycler_scrub command
    • pilon_polish.py command
    • --vcf option (#259, #271)
    • Sorry to anyone that actually used these – you can still find them in previous versions of Unicycler!
  • A couple new command line options:
    • --no_simple_bridges to turn off simple long-read bridging (#256)
    • --spades_options to provide additional options for SPAdes (#215, #279)
  • Added -m option to SPAdes call to fix issue with macOS v12 (ablab/spades#839)
  • A few bug fixes in long-read bridging (#181, #203, #245, #256).
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