diff --git a/topics/assembly/tutorials/mrsa-illumina/data-library.yaml b/topics/assembly/tutorials/mrsa-illumina/data-library.yaml index fda879aabc1e94..23881dd66ea5f1 100644 --- a/topics/assembly/tutorials/mrsa-illumina/data-library.yaml +++ b/topics/assembly/tutorials/mrsa-illumina/data-library.yaml @@ -14,18 +14,18 @@ items: items: - name: Genome Assembly of MRSA using Illumina MiSeq Data items: - - name: 'DOI: 10.5281/zenodo.4534098' + - name: 'DOI: 10.5281/zenodo.10669812' description: latest items: - url: https://zenodo.org/api/files/52e04e0d-851d-42ff-8dd9-932b38cb8ca8/DRR187559_1.fastqsanger.bz2 src: url ext: fastqsanger.bz2 - info: https://doi.org/10.5281/zenodo.4534098 + info: https://doi.org/10.5281/zenodo.10669812 - url: https://zenodo.org/api/files/52e04e0d-851d-42ff-8dd9-932b38cb8ca8/DRR187559_2.fastqsanger.bz2 src: url ext: fastqsanger.bz2 - info: https://doi.org/10.5281/zenodo.4534098 + info: https://doi.org/10.5281/zenodo.10669812 - url: https://zenodo.org/api/files/52e04e0d-851d-42ff-8dd9-932b38cb8ca8/DRR187567.fastq.bz2 src: url ext: fastq.bz2 - info: https://doi.org/10.5281/zenodo.4534098 + info: https://doi.org/10.5281/zenodo.10669812 diff --git a/topics/assembly/tutorials/mrsa-illumina/tutorial.md b/topics/assembly/tutorials/mrsa-illumina/tutorial.md index 428ffbfdbe89e1..c91300534bc3a4 100644 --- a/topics/assembly/tutorials/mrsa-illumina/tutorial.md +++ b/topics/assembly/tutorials/mrsa-illumina/tutorial.md @@ -2,7 +2,7 @@ layout: tutorial_hands_on title: Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data -zenodo_link: 'https://zenodo.org/record/4534098' +zenodo_link: 'https://zenodo.org/record/10669812' questions: - How to check the quality of the MiSeq data? - How to perform an assembly of a bacterial genome with MiSeq data? @@ -384,4 +384,4 @@ The total length and the GC content of the assembly are coherent with expectatio # Conclusion -In this tutorial, we prepared short reads, assembled them, and inspect the produced assembly for its quality. The assembly, even if uncomplete, is reasonable good to be used in downstream analysis, like [AMR gene detection]({% link topics/genome-annotation/tutorials/amr-gene-detection/tutorial.md %}) \ No newline at end of file +In this tutorial, we prepared short reads, assembled them, and inspect the produced assembly for its quality. The assembly, even if uncomplete, is reasonable good to be used in downstream analysis, like [AMR gene detection]({% link topics/genome-annotation/tutorials/amr-gene-detection/tutorial.md %}) diff --git a/topics/assembly/tutorials/mrsa-illumina/workflows/main_workflow-test.yml b/topics/assembly/tutorials/mrsa-illumina/workflows/main_workflow-test.yml index aacfb9ad86c549..f3c050d00105ee 100644 --- a/topics/assembly/tutorials/mrsa-illumina/workflows/main_workflow-test.yml +++ b/topics/assembly/tutorials/mrsa-illumina/workflows/main_workflow-test.yml @@ -3,11 +3,11 @@ job: DRR187559_1: class: File - location: https://zenodo.org/record/4534098/files/DRR187559_1.fastqsanger.bz2 + location: https://zenodo.org/record/10669812/files/DRR187559_1.fastqsanger.bz2 filetype: fastqsanger.bz2 DRR187559_2: class: File - location: https://zenodo.org/record/4534098/files/DRR187559_2.fastqsanger.bz2 + location: https://zenodo.org/record/10669812/files/DRR187559_2.fastqsanger.bz2 filetype: fastqsanger.bz2 outputs: fastp_json: diff --git a/topics/assembly/tutorials/mrsa-nanopore/data-library.yaml b/topics/assembly/tutorials/mrsa-nanopore/data-library.yaml index 61e68065fdbe12..6b9c5e8764960a 100644 --- a/topics/assembly/tutorials/mrsa-nanopore/data-library.yaml +++ b/topics/assembly/tutorials/mrsa-nanopore/data-library.yaml @@ -14,18 +14,18 @@ items: items: - name: Genome Assembly of MRSA using Oxford Nanopore MinION Data items: - - name: 'DOI: 10.5281/zenodo.4534098' + - name: 'DOI: 10.5281/zenodo.10669812' description: latest items: - url: https://zenodo.org/api/files/52e04e0d-851d-42ff-8dd9-932b38cb8ca8/DRR187559_1.fastqsanger.bz2 src: url ext: fastqsanger.bz2 - info: https://doi.org/10.5281/zenodo.4534098 + info: https://doi.org/10.5281/zenodo.10669812 - url: https://zenodo.org/api/files/52e04e0d-851d-42ff-8dd9-932b38cb8ca8/DRR187559_2.fastqsanger.bz2 src: url ext: fastqsanger.bz2 - info: https://doi.org/10.5281/zenodo.4534098 + info: https://doi.org/10.5281/zenodo.10669812 - url: https://zenodo.org/api/files/52e04e0d-851d-42ff-8dd9-932b38cb8ca8/DRR187567.fastq.bz2 src: url ext: fastq.bz2 - info: https://doi.org/10.5281/zenodo.4534098 + info: https://doi.org/10.5281/zenodo.10669812 diff --git a/topics/assembly/tutorials/mrsa-nanopore/tutorial.md b/topics/assembly/tutorials/mrsa-nanopore/tutorial.md index f0286b482cf64b..446c57418ed53b 100644 --- a/topics/assembly/tutorials/mrsa-nanopore/tutorial.md +++ b/topics/assembly/tutorials/mrsa-nanopore/tutorial.md @@ -2,7 +2,7 @@ layout: tutorial_hands_on title: Genome Assembly of MRSA using Oxford Nanopore MinION Data -zenodo_link: 'https://zenodo.org/record/4534098' +zenodo_link: 'https://zenodo.org/record/10669812' questions: - How to check the quality of the MinION data? - How to perform an assembly with MinION data?