hifi-assembly-workflow

Nextflow workflow for Hifi Genome Assembly

https://github.com/australianbiocommons/hifi-assembly-workflow

Science Score: 57.0%

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CITATION.cff file
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codemeta.json file
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DOI references
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Low similarity (6.8%) to scientific vocabulary

Last synced: 10 months ago · JSON representation ·

Repository

Nextflow workflow for Hifi Genome Assembly

Basic Info

Host: GitHub
Owner: AustralianBioCommons
License: mit
Language: Nextflow
Default Branch: master
Homepage: https://australianbiocommons.github.io/hifi-assembly-workflow/
Size: 516 KB

Statistics

Stars: 0
Watchers: 1
Forks: 0
Open Issues: 1
Releases: 1

Created almost 3 years ago · Last pushed almost 2 years ago

Metadata Files

Readme Changelog License Citation Codemeta

HiFi de novo genome assembly workflow

HiFi-assembly-workflow is a bioinformatics pipeline that can be used to analyse Pacbio CCS reads for de novo genome assembly using PacBio Circular Consensus Sequencing (CCS) reads. This workflow is implemented in Nextflow and has 3 major sections.

Please refer to the following documentation for detailed description of each workflow section:

General recommendations

A more detailed module and workflow description as well as execution examples on Gadi and Setonix are available here.

Attributions

This work was developed at AGRF and supported by the Australian BioCommons via Bioplatforms Australia funding, the Australian Research Data Commons (https://doi.org/10.47486/PL105) and the Queensland Government RICF programme. Bioplatforms Australia and the Australian Research Data Commons are enabled by the National Collaborative Research Infrastructure Strategy (NCRIS).

The documentation in this repository is based on Australian BioCommons guidelines.

Owner

Name: AustralianBioCommons
Login: AustralianBioCommons
Kind: organization
Email: systems@biocommons.org.au

Website: https://www.biocommons.org.au/
Repositories: 17
Profile: https://github.com/AustralianBioCommons

Documentation for the development, deployment and/or optimisation of key community-endorsed bioinformatics tools and workflows

Citation (CITATION.cff)

cff-version: 1.1.0
message: "Please cite as below."
authors:
  - family-names: Kasinadhuni
    given-names: Naga
  - family-names: Al Bkhetan
    given-names: Ziad
    orcid: https://orcid.org/0000-0002-4032-5331
  - family-names: Zakrzewski
    given-names: Martha
  - family-names: Chan
    given-names: Kenneth
  - family-names: Winter
    given-names: Uwe
  - family-names: Gustafsson
    given-names: Johan
    orcid: https://orcid.org/0000-0002-2977-5032
title: "HiFi de novo genome assembly workflow"
version: 1.1.0
doi: [DOI goes here]
date-released: 2023-08-30
repository-code: https://github.com/AustralianBioCommons/hifi-assembly-workflow

CodeMeta (codemeta.json)

{
  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
  "@type": "SoftwareSourceCode",
  "license": "https://spdx.org/licenses/MIT",
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  "dateModified": "2023-08-30",
  "name": "HiFi de novo genome assembly workflow",
  "version": "1.1.0",
  "description": "HiFi-assembly-workflow is a bioinformatics pipeline that can be used to analyse Pacbio CCS reads for de novo genome assembly using PacBio Circular Consensus Sequencing (CCS) reads.",
  "applicationCategory": "Genomics",
  "programmingLanguage": [
    "Nextflow"
  ],
  "author": [
    {
      "@type": "Person",
      "givenName": "Naga ",
      "familyName": "Kasinadhuni",
      "affiliation": {
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      }
    },
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      "@type": "Person",
      "givenName": "Ziad ",
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        "@type": "Organization",
        "name": "Australian BioCommons / University of Melbourne"
      }
    },
    {
      "@type": "Person",
      "givenName": "Martha ",
      "familyName": "Zakrzewski",
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    },
    {
      "@type": "Person",
      "givenName": "Kenneth ",
      "familyName": "Chan",
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    {
      "@type": "Person",
      "givenName": "Uwe",
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  "contributor": [
    {
      "@type": "Person",
      "givenName": "Johan ",
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        "@type": "Organization",
        "name": "Australian BioCommons / University of Melbourne"
      }
    }
  ]
}

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