shovill | ️ Assemble bacterial isolate genomes from Illumina | Genomics library

 by   tseemann Perl Version: v1.1.0 License: GPL-3.0

kandi X-RAY | shovill Summary

kandi X-RAY | shovill Summary

shovill is a Perl library typically used in Artificial Intelligence, Genomics applications. shovill has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

The SPAdes genome assembler has become the de facto standard de novo genome assembler for Illumina whole genome sequencing data of bacteria and other small microbes. SPAdes was a major improvement over previous assemblers like Velvet, but some of its components can be slow and it traditionally did not handle overlapping paired-end reads well. Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. :warning: Shovill is for isolate data only, primarily small haploid organisms. It will NOT work on metagenomes or larger genomes. Please use Megahit directly instead.

            kandi-support Support

              shovill has a low active ecosystem.
              It has 121 star(s) with 30 fork(s). There are 15 watchers for this library.
              It had no major release in the last 12 months.
              There are 30 open issues and 119 have been closed. On average issues are closed in 44 days. There are 2 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of shovill is v1.1.0

            kandi-Quality Quality

              shovill has 0 bugs and 0 code smells.

            kandi-Security Security

              shovill has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              shovill code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              shovill is licensed under the GPL-3.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              shovill releases are available to install and integrate.
              Installation instructions are not available. Examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi's functional review helps you automatically verify the functionalities of the libraries and avoid rework.
            Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of shovill
            Get all kandi verified functions for this library.

            shovill Key Features

            No Key Features are available at this moment for shovill.

            shovill Examples and Code Snippets

            No Code Snippets are available at this moment for shovill.

            Community Discussions


            Snakemake How to design downstream rules on empty output files?
            Asked 2021-Aug-27 at 16:00

            I am wondering how to deal with empty output files in downstream rules. An assembly of a short read fastq data with SHOVILL can fail and produce a 0-byte contigs.fa

            If genome annotation with PROKKA is run on a 0-byte file it returns an error:



            Answered 2021-Aug-27 at 16:00

            I can think of two approaches, neither is perfect.

            The first is basically what you did: use bash to work around. However, I would suggest the -s file test operator. This way, you still get notified of a genuine error from prokka:


            Community Discussions, Code Snippets contain sources that include Stack Exchange Network


            No vulnerabilities reported

            Install shovill

            You can download it from GitHub.


            Please file questions, bugs or ideas to the Issue Tracker.
            Find more information at:

            Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items

            Find more libraries

            Stay Updated

            Subscribe to our newsletter for trending solutions and developer bootcamps

            Agree to Sign up and Terms & Conditions

            Share this Page

            share link