diff --git a/topics/sequence-analysis/images/HistogramReadlength.png b/topics/sequence-analysis/images/HistogramReadlength.png index 97845542041d48..752c4fe24b8278 100644 Binary files a/topics/sequence-analysis/images/HistogramReadlength.png and b/topics/sequence-analysis/images/HistogramReadlength.png differ diff --git a/topics/sequence-analysis/images/LengthvsQualityScatterPlot_dot.png b/topics/sequence-analysis/images/LengthvsQualityScatterPlot_dot.png index 53a75bb3a30dd0..a7fb172d06855b 100644 Binary files a/topics/sequence-analysis/images/LengthvsQualityScatterPlot_dot.png and b/topics/sequence-analysis/images/LengthvsQualityScatterPlot_dot.png differ diff --git a/topics/sequence-analysis/images/quality-control/HistogramReadlength.png b/topics/sequence-analysis/images/quality-control/HistogramReadlength.png index 97845542041d48..752c4fe24b8278 100644 Binary files a/topics/sequence-analysis/images/quality-control/HistogramReadlength.png and b/topics/sequence-analysis/images/quality-control/HistogramReadlength.png differ diff --git a/topics/sequence-analysis/images/quality-control/LengthvsQualityScatterPlot_dot.png b/topics/sequence-analysis/images/quality-control/LengthvsQualityScatterPlot_dot.png index 53a75bb3a30dd0..a7fb172d06855b 100644 Binary files a/topics/sequence-analysis/images/quality-control/LengthvsQualityScatterPlot_dot.png and b/topics/sequence-analysis/images/quality-control/LengthvsQualityScatterPlot_dot.png differ diff --git a/topics/sequence-analysis/tutorials/quality-control/tutorial.md b/topics/sequence-analysis/tutorials/quality-control/tutorial.md index 58be8eaf8a2868..c961abcf02cb78 100644 --- a/topics/sequence-analysis/tutorials/quality-control/tutorial.md +++ b/topics/sequence-analysis/tutorials/quality-control/tutorial.md @@ -36,6 +36,7 @@ contributors: - r1corre - stephanierobin - erasmusplus + - neoformit --- @@ -878,7 +879,7 @@ In case of long reads, we can check sequence quality with [Nanoplot](https://git > https://zenodo.org/api/files/ff9aa6e3-3d69-451f-9798-7ea69b475989/m64011_190830_220126.Q20.subsample.fastq.gz > ``` > -> 3. {% tool [Nanoplot](toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1) %} with the following parameters +> 3. {% tool [Nanoplot](toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0) %} with the following parameters > - {% icon param-files %} *"files"*: `m64011_190830_220126.Q20.subsample.fastq.gz` > - *"Options for customizing the plots created"* > - {% icon param-select %} *"Specify the bivariate format of the plots."*: `dot`, `kde` @@ -912,7 +913,7 @@ In case of long reads, we can check sequence quality with [Nanoplot](https://git This plot shows the distribution of fragment sizes in the file that was analyzed. Unlike most of Illumina runs, long reads have a variable length and this will show the relative amounts of each different size of sequence fragment. -In this example, the distribution of read length is centered near 15kbp but the results can be very different depending of your experiment. +In this example, the distribution of read length is centered near 18kbp but the results can be very different depending of your experiment. ![Histogram of read lengths](../../images/quality-control/HistogramReadlength.png "Histogram of read length") @@ -1087,6 +1088,6 @@ Quality control steps are similar for any type of sequencing data: - Quality assessment with tools like: - *Short Reads*: {% tool [FASTQE](toolshed.g2.bx.psu.edu/repos/iuc/fastqe/fastqe/0.2.6+galaxy2) %} - *Short+Long*: {% tool [FASTQC](toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0) %} - - *Long Reads*: {% tool [Nanoplot](toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1) %} + - *Long Reads*: {% tool [Nanoplot](toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0) %} - *Nanopore only*: {% tool [PycoQC](toolshed.g2.bx.psu.edu/repos/iuc/pycoqc/pycoqc/2.5.2+galaxy0) %} - Trimming and filtering for **short reads** with a tool like **Cutadapt** {% icon tool %}