From 400fb9c7aa53001937be81af42e2965083a3bb16 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Fri, 15 Nov 2024 10:29:56 +0100 Subject: [PATCH 1/4] Fix MRSA nanopore tutorial CYOA Thanks to new linting --- .../assembly/tutorials/mrsa-nanopore/tutorial.md | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/topics/assembly/tutorials/mrsa-nanopore/tutorial.md b/topics/assembly/tutorials/mrsa-nanopore/tutorial.md index eb9f2e0b43cc58..53ba13edb3feb7 100644 --- a/topics/assembly/tutorials/mrsa-nanopore/tutorial.md +++ b/topics/assembly/tutorials/mrsa-nanopore/tutorial.md @@ -153,7 +153,9 @@ The dataset is a FASTQ file. {% include _includes/cyoa-choices.html option1="Without Illumina MiSeq data" option2="With Illumina MiSeq data" default="Without Illumina MiSeq data" text="Do you have associated Illumina MiSeq data?" disambiguation="miseq"%} -
+ + +
> Illumina Data upload > 1. {% tool [Import](upload1) %} the files from [Zenodo]({{ page.zenodo_link }}) or from the shared data library @@ -197,7 +199,7 @@ FastQC combines quality statistics from all separate reads and combines them in ![FastQC plot showing reads that mostly stay in the read](./images/fastqc.png) -
+
Here, we are going to trim the Illumina data using **fastp** ({% cite Chen2018 %}): @@ -228,7 +230,7 @@ Here, we are going to trim the Illumina data using **fastp** ({% cite Chen2018 % Depending on the analysis it could be possible that a certain quality or length is needed. The reads can be filtered using the [Filtlong](https://github.com/rrwick/Filtlong) tool. In this training all reads below 1000bp will be filtered. -
+
When Illumina reads are available, we can use them **if they are good Illumina reads (high depth and complete coverage)** as external reference. In this case, Filtlong ignores the Phred quality scores and instead judges read quality using k-mer matches to the reference (a more accurate gauge of quality). @@ -240,7 +242,7 @@ When Illumina reads are available, we can use them **if they are good Illumina r > - In *"Output thresholds"*: > - *"Min. length"*: `1000` > ->
+>
> - In *"External references"*: > - {% icon param-file %} *"Reference Illumina read"*: **fastp** `Read 1 output` > - {% icon param-file %} *"Reference Illumina read"*: **fastp** `Read 2 output` @@ -431,7 +433,7 @@ QUAST outputs assembly metrics as an HTML file with metrics and graphs. > {: .solution} {: .question} -
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## Assembly Polishing @@ -513,4 +515,4 @@ GC (%) | 32.91 | 32.84 # Conclusion -In this tutorial, we prepared long reads (using short reads if we had some) assembled them, inspect the produced assembly for its quality, and polished it (if short reads where provided). 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 long reads (using short reads if we had some) assembled them, inspect the produced assembly for its quality, and polished it (if short reads where provided). 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 %}) From d8b628e5b7ea65535da9709a1ac0acb76a8d8cc4 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Fri, 15 Nov 2024 10:47:47 +0100 Subject: [PATCH 2/4] incorrect parameter name --- topics/assembly/tutorials/mrsa-nanopore/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/assembly/tutorials/mrsa-nanopore/tutorial.md b/topics/assembly/tutorials/mrsa-nanopore/tutorial.md index 53ba13edb3feb7..654be1ecae389a 100644 --- a/topics/assembly/tutorials/mrsa-nanopore/tutorial.md +++ b/topics/assembly/tutorials/mrsa-nanopore/tutorial.md @@ -218,7 +218,7 @@ Here, we are going to trim the Illumina data using **fastp** ({% cite Chen2018 % > - In *"Read Modification Options"*: > - In *"Per read cuitting by quality options"*: > - *Cut by quality in front (5')*: `Yes` -> - *Cut by quality in front (3')*: `Yes` +> - *Cut by quality in tail (3')*: `Yes` > - *Cutting window size*: `4` > - *Cutting mean quality*: `20` > - In *"Output Options"*: From b1aaa25a4856646a06a0ebac5e7b7e9e58dbcc09 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Fri, 15 Nov 2024 11:40:12 +0100 Subject: [PATCH 3/4] jbrowse is no longer used in this tutorial --- topics/assembly/tutorials/mrsa-nanopore/tutorial.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/topics/assembly/tutorials/mrsa-nanopore/tutorial.md b/topics/assembly/tutorials/mrsa-nanopore/tutorial.md index 654be1ecae389a..f87381237916d3 100644 --- a/topics/assembly/tutorials/mrsa-nanopore/tutorial.md +++ b/topics/assembly/tutorials/mrsa-nanopore/tutorial.md @@ -22,8 +22,6 @@ tags: - nanopore - assembly - amr -- gmod -- jbrowse1 - microgalaxy edam_ontology: - topic_0196 # Sequence Assembly From 78a62d8a8738b7cf3c123eff0caf6b4ffc0d28bf Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Fri, 15 Nov 2024 12:01:37 +0100 Subject: [PATCH 4/4] remove unnecessary space --- topics/microbiome/tutorials/beer-data-analysis/tutorial.md | 1 - 1 file changed, 1 deletion(-) diff --git a/topics/microbiome/tutorials/beer-data-analysis/tutorial.md b/topics/microbiome/tutorials/beer-data-analysis/tutorial.md index 651349a30989ad..3f5b45aba42d31 100644 --- a/topics/microbiome/tutorials/beer-data-analysis/tutorial.md +++ b/topics/microbiome/tutorials/beer-data-analysis/tutorial.md @@ -578,7 +578,6 @@ The species identified for Chimay beers are (from the most abundant to the least - *Saccharomyces cerevisiae* - *Saccharomyces mikatea*: a species generally used in winemaking ({% cite bellon2013introducing %}) - *Kazachstania martiniae*: *Kazachstania* is a genus from the family Saccharomycetaceaethe. - - *Saccharomyces kudriavzevii* - *Brettanomyces bruxellensis*