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Fix odd bzip2 record #4732

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Feb 20, 2024
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Fix odd bzip2 record #4732

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8 changes: 4 additions & 4 deletions topics/assembly/tutorials/mrsa-illumina/data-library.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
4 changes: 2 additions & 2 deletions topics/assembly/tutorials/mrsa-illumina/tutorial.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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?
Expand Down Expand Up @@ -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 %})
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 %})
4 changes: 2 additions & 2 deletions topics/assembly/tutorials/mrsa-illumina/workflows/main_workflow-test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down
8 changes: 4 additions & 4 deletions topics/assembly/tutorials/mrsa-nanopore/data-library.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
2 changes: 1 addition & 1 deletion topics/assembly/tutorials/mrsa-nanopore/tutorial.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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?
Expand Down
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