# Unable to run Unicycler or ABySS

**URL:** <https://help.galaxyproject.org/t/unable-to-run-unicycler-or-abyss/4546>\
**Category:** usegalaxy.org support\
**Tags:** gtn-tutorial, tool-deprecated, single-cell\
**Created:** [October 1, 2020, 8:39pm UTC](https://help.galaxyproject.org/t/unable-to-run-unicycler-or-abyss/4546 "2020-10-01T20:39:45Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![mnyoung](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/mnyoung/32/1879_2.png) [@mnyoung](https://help.galaxyproject.org/u/mnyoung)\
**Post date:** [October 1, 2020, 8:39pm UTC](https://help.galaxyproject.org/t/unable-to-run-unicycler-or-abyss/4546/1 "2020-10-01T20:39:45Z")

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Hello,

I’m new to Galaxy, so I hope this is the correct way to post a question. I’m attempting to assemble a bacterial genome using a pair of Illumina reads and a PacBio read with ABySS and with Unicycler. I’ve tried doing this in several different ways according to the information included in the tool descriptions, but both assemblers fail to run and give a tool error. What are the correct file types and suffixes for each read in each assembler? (by suffixes, I mean the ending of “1” and “2” for paired short reads, for example).

Thank you for your help, I look forward to learning more about Galaxy.

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**Author:** ![mnyoung](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/mnyoung/32/1879_2.png) [@mnyoung](https://help.galaxyproject.org/u/mnyoung)\
**Post date:** [October 15, 2020, 3:01am UTC](https://help.galaxyproject.org/t/unable-to-run-unicycler-or-abyss/4546/2 "2020-10-15T03:01:50Z")

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Hi, I apologize, but I’m unfortunately still having difficulty resolving this issue. I would really appreciate any suggestions. Thanks!

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [January 13, 2021, 12:49am UTC](https://help.galaxyproject.org/t/unable-to-run-unicycler-or-abyss/4546/3 "2021-01-13T00:49:10Z")

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`Unicycler` is functional. `ABySS` has been removed.

GTN Tutorial for assembly (including `Unicycler`):

> **[Galaxy Training: Assembly](https://training.galaxyproject.org/training-material/topics/assembly/)**
>
> DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these field...

> [@ABySS fungal de novo genome assembly: Update, ABySS removed from usegalaxy.org, alternative usegalaxy.eu](https://help.galaxyproject.org/t/abyss-fungal-de-novo-genome-assembly-update-abyss-removed-from-usegalaxy-org-alternative-usegalaxy-eu/3415/2):
>
> **Update**
> 
> The assembler ABySS has been technically problematic at [UseGalaxy.org](http://UseGalaxy.org) for some time now.
> 
> The tool has been removed from [UseGalaxy.org](http://UseGalaxy.org).
> 
> An alternative usegalaxy.\* server for this tool is [UseGalaxy.eu](http://UseGalaxy.eu)

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [February 10, 2023, 8:13pm UTC](https://help.galaxyproject.org/t/unable-to-run-unicycler-or-abyss/4546/4 "2023-02-10T20:13:54Z")

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