diff --git a/course_modules_2023/IGV/IGV.pdf b/course_modules_2023/IGV/IGV.pdf deleted file mode 100644 index 29ff987..0000000 Binary files a/course_modules_2023/IGV/IGV.pdf and /dev/null differ diff --git a/course_modules_2023/IGV/README.md b/course_modules_2023/IGV/README.md deleted file mode 100644 index 8b13789..0000000 --- a/course_modules_2023/IGV/README.md +++ /dev/null @@ -1 +0,0 @@ - diff --git a/course_modules_2023/Long_Read_Analysis/Oxford_Nanopore_2023_plus_analysis.pdf b/course_modules_2023/Long_Read_Analysis/Oxford_Nanopore_2023_plus_analysis.pdf deleted file mode 100644 index f2eea96..0000000 Binary files a/course_modules_2023/Long_Read_Analysis/Oxford_Nanopore_2023_plus_analysis.pdf and /dev/null differ diff --git a/course_modules_2023/Long_Read_Analysis/README.md b/course_modules_2023/Long_Read_Analysis/README.md deleted file mode 100644 index 8b13789..0000000 --- a/course_modules_2023/Long_Read_Analysis/README.md +++ /dev/null @@ -1 +0,0 @@ - diff --git a/course_modules_2023/Long_Read_Analysis/WCS Intro to NGS Oxford Nanopore Analysis session.ipynb b/course_modules_2023/Long_Read_Analysis/WCS Intro to NGS Oxford Nanopore Analysis session.ipynb deleted file mode 100644 index 3167bf5..0000000 --- a/course_modules_2023/Long_Read_Analysis/WCS Intro to NGS Oxford Nanopore Analysis session.ipynb +++ /dev/null @@ -1,276 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "id": "c9aff88d", - "metadata": {}, - "source": [ - "## MinION bioinformatics practical: download software & assemble a bacterial genome " - ] - }, - { - "cell_type": "markdown", - "id": "638d6608", - "metadata": {}, - "source": [ - "In this course, we will use miniasm, which is a very quick assembler – but the assemblies will be less accurate as we do not include an error correction step. It’s a good way to check you’re heading in the right direction in your research, but you should consider switching to more accurate assemblers as your project progresses. When & which assembler will depend on your specific research question. \n", - "\n", - "We will also install some software from the version control website Github. This software is open access and free to use. Github can be a great resource for finding and installing bioinformatics software, but as always, do take care that what you are installing is genuine, safe to use, and suitable for your operating system and computer specifications \n", - "\n", - "Getting started: \n", - "\n", - "Open a terminal and check you are in the home directory \n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "4aadb6b4", - "metadata": {}, - "outputs": [], - "source": [ - "pwd" - ] - }, - { - "cell_type": "markdown", - "id": "0abd104a", - "metadata": {}, - "source": [ - "Make a new directory called longread (all one word) and cd into it. (You can do this in two steps or you can chain them together using &&" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "fb026134", - "metadata": {}, - "outputs": [], - "source": [ - "mkdir longread && cd longread " - ] - }, - { - "cell_type": "markdown", - "id": "3390b85d", - "metadata": {}, - "source": [ - "###### Installing software\n", - "\n", - "You will need to install a dependency package. Type in the following:\n", - "\n", - "sudo apt-get install libz-dev\n", - "\n", - "If prompted for a password, use “manager”\n", - "\n", - "Open a new tab in a browser window and search for (Google) miniasm\n", - "\n", - "Click on top hit – github.com/lh3/miniasm\n", - "\n", - "Find the text below on the webpage, copy it and paste it into your terminal window (You may need to use ctrl+ins and shift+ins instead of ctrl+c and ctrl+v)\n", - "\n", - "git clone https://github.com/lh3/miniasm && (cd miniasm && make) \n", - "\n", - "minimap2 should already be installed as part of an earlier session on the course - if it is not, do the same for\n", - "\n", - "git clone https://github.com/lh3/minimap2 && (cd minimap2 && make)\n", - "\n", - "\n", - "###### Making an assembly\n", - "\n", - "Check you are working in the longread folder and you have three subfolders, minimap2, miniasm.\n", - "\n", - "You’ve been given some long read Oxford Nanopore data in your VM. Check that you have this data available to you. This should be found in the directory ONT_data" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "f9a17d21", - "metadata": {}, - "outputs": [], - "source": [ - "ls ~/ONT_data" - ] - }, - { - "cell_type": "markdown", - "id": "c403bd8f", - "metadata": {}, - "source": [ - "You are now ready to run your assembly – it will probably take 10-15 minutes. First, use minimap2 to map the reads to each other, creating overlaps. Don’t forget, you will need to either copy (cp) the reads to the directory you are working in, or, a better way is to give the path to where your reads are stored (this will use a lot less of your computer’s storage space)then use miniasm to assemble the overlapped reads\n", - "\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "3c5aedaf", - "metadata": {}, - "outputs": [], - "source": [ - "minimap2/minimap2 -x ava-ont /your/path/barcode1.fastq /your/path/barcode1.fastq > barcode1.paf" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "d4a85917", - "metadata": {}, - "outputs": [], - "source": [ - "miniasm/miniasm –f /your/path/barcode1.fastq barcode1.paf > barcode1.gfa" - ] - }, - { - "cell_type": "markdown", - "id": "5c1b8cd5", - "metadata": {}, - "source": [ - "To get the reads from .gfa format to .fasta (also called .fa), you’ll need to use this awk command (be careful to get it exactly right)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "54e911e8", - "metadata": {}, - "outputs": [], - "source": [ - "awk '$1==\"S\" {print \">\"$2\"\\n\"$3}' barcode1.gfa > barcode1.fa" - ] - }, - { - "cell_type": "markdown", - "id": "04b5dafb", - "metadata": {}, - "source": [ - "You can now check out your new assembly file. Try some of the following:" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "9becfd8b", - "metadata": {}, - "outputs": [], - "source": [ - "wc\n", - "head\n", - "ls –l\n", - "tail" - ] - }, - { - "cell_type": "markdown", - "id": "86ec1e52", - "metadata": {}, - "source": [ - "You can also use scripts to assess your assembly. Here, we have already installed a script called assembly-stats " - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "40d94130", - "metadata": {}, - "outputs": [], - "source": [ - "assembly-stats barcode1.fa" - ] - }, - { - "cell_type": "markdown", - "id": "d20949bc", - "metadata": {}, - "source": [ - "You can find this at https://github.com/sanger-pathogens/assembly-stats if you want to install it on your own machines. It’s slightly more complicated to install than what we have done so far, but it’s similar, and there are instructions on the website. Just make sure to start with git clone . To use assembly stats, type in the name of your fasta or fastq file (instead of reads.fa above)" - ] - }, - { - "cell_type": "markdown", - "id": "71565f16", - "metadata": {}, - "source": [ - "## Next steps\n", - "\n", - "There are two other sample fastqs in the ONT_data folder. In order to assemble these in a short time frame, and without using too much of your computer’s memory, you will need to down-sample the data. You can choose which sample to work on, or try more than one, or try a couple of different depths of coverage if you have time. \n", - "\n", - "Use the tool chopper, which is already installed for you. You can filter your data on quality score (using -q) or length (using -l) - you might like to filter to remove all reads shorter than 500bp, or with quality score higher than ten. Use chopper -h to read the help file. \n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "02ec1758", - "metadata": {}, - "outputs": [], - "source": [ - "cat barcode2.fastq | chopper -q 10 -l 500 > barcode2_filtered.fastq" - ] - }, - { - "cell_type": "markdown", - "id": "3b47aa5f", - "metadata": {}, - "source": [ - "###### Things to consider when filtering or downsampling data for assembly:\n", - "\n", - "\n", - "You can check how much data you have using the size of your assembly from the first part of the experiment, and \n", - "running assembly-stats on your filtered fastq file.\n", - " \n", - "e.g. assembly-stats your_assembly_sample_1.fa\n", - "n=4000000 \n", - "\n", - "Your assembly is 4Mb\n", - "\n", - "e.g. assembly-stats your_filtered.fastq\n", - "n=100000000 \n", - "\n", - "Your filtered fastq is 100Mb. This gives you a \"theoretical depth of coverage\" (TDOC) of 25x, i.e. your dataset is 25x your genome size. \n", - "\n", - "You should typically provide an absolute minimum of 20x TDOC when running an assembly. For many applications, it’s not wise to use lower than 30x.\n", - "There’s no upper limit on the maximum depth of coverage, but you are likely to find more than 100x won’t finish within this session (or length of this course! Or within the capability of your laptop!)\n", - "\n", - "\n", - "Once you have down-sampled your data, go through the steps in the first task to create an assembly and assess its size.\n" - ] - }, - { - "cell_type": "markdown", - "id": "53bc115b", - "metadata": {}, - "source": [ - "###### Acknowledgements\n", - "\n", - "With thanks to the following people who were involved in generating the data used today: \n", - "\n", - "Trevor Lawley & team, Yan Shao, Sanger Long Read sequencing team\n", - "\n", - "This is unpublished data and should not be used for anything outside this session, and practicing the skills you have learnt on this course" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.9.6" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/course_modules_2023/Long_Read_Analysis/WCS Intro to NGS Oxford Nanopore Analysis session.pdf b/course_modules_2023/Long_Read_Analysis/WCS Intro to NGS Oxford Nanopore Analysis session.pdf deleted file mode 100644 index b0fcf4e..0000000 Binary files a/course_modules_2023/Long_Read_Analysis/WCS Intro to NGS Oxford Nanopore Analysis session.pdf and /dev/null differ diff --git a/course_modules_2023/NGS_Data_Formats_and_QC/README.md b/course_modules_2023/NGS_Data_Formats_and_QC/README.md deleted file mode 100644 index 8b13789..0000000 --- a/course_modules_2023/NGS_Data_Formats_and_QC/README.md +++ /dev/null @@ -1 +0,0 @@ - diff --git a/course_modules_2023/NGS_Data_Formats_and_QC/data_formats_practical.pdf b/course_modules_2023/NGS_Data_Formats_and_QC/data_formats_practical.pdf deleted file mode 100644 index 32bb0f5..0000000 Binary files a/course_modules_2023/NGS_Data_Formats_and_QC/data_formats_practical.pdf and /dev/null differ diff --git a/course_modules_2023/NGS_Data_Formats_and_QC/data_formats_slides.pdf b/course_modules_2023/NGS_Data_Formats_and_QC/data_formats_slides.pdf deleted file mode 100644 index 2b5fe29..0000000 Binary files a/course_modules_2023/NGS_Data_Formats_and_QC/data_formats_slides.pdf and /dev/null differ diff --git a/course_modules_2023/NGS_Data_Formats_and_QC/qc_slides.pdf b/course_modules_2023/NGS_Data_Formats_and_QC/qc_slides.pdf deleted file mode 100644 index 23f2aec..0000000 Binary files a/course_modules_2023/NGS_Data_Formats_and_QC/qc_slides.pdf and /dev/null differ diff --git a/course_modules_2023/README.md b/course_modules_2023/README.md deleted file mode 100644 index d69a790..0000000 --- a/course_modules_2023/README.md +++ /dev/null @@ -1,106 +0,0 @@ -# Course Modules Directory Instructions for Training Team - -## Purpose -This directory contains all course module files, including presentations, practical manuals, and supplementary materials essential for delivering the course content effectively. - -## Suggested File Types -- Presentation slides (PowerPoint, Word Documents, PDF) -- Practical manuals (Markdown, PDF) -- Supplementary instructional materials
- -**Important Note**: It is highly advised to convert PowerPoint and Word Documents into PDFs before uploading. - -## Best Practices for Naming Conventions -To ensure clarity and consistency, please follow these naming conventions for your files: -- Use descriptive names that reflect the content (e.g., `module_1_overview.pptx`, `module_2_practical_manual.md`). -- Use lowercase letters and separate words with underscores (_) for better readability. -- Include version numbers if necessary (e.g., `module_v1.0.pdf`). - -## Steps to Add Files via GitHub Interface -1. **Navigate to the Repository:** Go to the GitHub repository for the course. -2. **Select the `course_modules` Directory:** Click on the `course_modules` folder to open it. -3. **Click on "Add file":** On the right-hand side, you’ll see an option labelled **Add file**. -4. **Choose "Upload files":** From the dropdown menu, select **Upload files**. -5. **Drag and Drop or Select Files:** You can either drag and drop your files into the space provided or click **choose your files** to upload them from your computer. -6. **Commit Changes:** Once your files are uploaded, scroll down to the **Commit changes** section. - - Enter a brief description of the changes in the commit message field (e.g., "Adding new module materials"). - - Click **Commit changes** to finalize your upload. - -## Overview of Manual Development -Each module manual should encompass the following essential components to ensure a comprehensive learning experience: - -1. **Background of the Topic:** - - Provide a thorough explanation of key concepts related to the module. - - Discuss the significance and relevance of the topic in the broader context of the field. - - Include historical background or foundational theories where applicable. - - Utilize visuals, such as diagrams or charts, to enhance understanding. - -2. **Learning Outcomes:** - - Clearly articulate the expected learning outcomes for the module. - - Detail specific skills or knowledge participants should gain upon completion. - - Consider framing outcomes in measurable terms to facilitate assessment (e.g., "By the end of this module, participants will be able to analyze genomic sequences using specific software tools."). - - Include any prerequisites or foundational knowledge needed to achieve these outcomes. - -3. **Detailed Steps or Exercises:** - - Provide comprehensive, step-by-step instructions or exercises that participants should follow during the training. - - Ensure each step is clearly numbered or bulleted for easy navigation. - - Incorporate practical applications or case studies that relate to the theoretical content covered. - - Include checkpoints or self-assessment questions at various stages to reinforce learning and allow participants to gauge their understanding. - - Specify any required materials, tools, or software for each exercise, along with troubleshooting tips where necessary. - - Encourage participants to document their findings and reflections to enhance the learning experience. - -By including these components, the module manuals will facilitate a deeper understanding of the content and provide participants with the tools necessary for practical application. - -## Manual Template - -For your reference, please download the manual template [here](https://docs.google.com/document/d/1k41dVLRCnSNs5eA0Vf7lslfAlEJWJNUW/edit?usp=sharing&ouid=104730864282583984566&rtpof=true&sd=true). Ensure that your manual is comprehensive and includes all necessary information. - -For formatting guidance, kindly refer to the detailed [Style and Writing Guide](https://drive.google.com/file/d/1siD1TKXp1tqkJl-WIt27Zzl8lj-jgtEy/view?usp=sharing) and [Branding Guide](https://drive.google.com/file/d/1cNqrzYZPhD7Z_IVLDhf9XolTFqNPLc48/view?usp=sharing). - -## Presentation Slides - -It is mandatory to include the Wellcome Connecting Science logo in your presentations. You may choose between the following logo options: - -- [Wellcome Connecting Science Black Font Logo](https://drive.google.com/file/d/1MEBaLjZTkzt3S2IBbIhEGEJxIhdiARjP/view?usp=sharing) -- [Wellcome Connecting Science White Font Logo](https://drive.google.com/file/d/1A-HIS0fHFIylwYz_k71xiVWlrWzawf_Z/view?usp=sharing) - -Additionally, please review the [PowerPoint Presentation Template Guide](https://docs.google.com/presentation/d/15DPvtwYD-H7YiuNXXLPOa2leQ4ot_TYO/edit?usp=sharing&ouid=104730864282583984566&rtpof=true&sd=true) for further instructions. - -## Laboratory Manual Content Examples -- **Step-by-Step Instructions or Exercises:** Participants are expected to follow specific protocols during the lab sessions to ensure consistency and accuracy in their work. Each laboratory session should clearly outline: - - The objectives of the exercises. - - Detailed methodologies, including equipment and materials needed. - - Safety protocols to follow during the experiments. - - Data collection and analysis methods. - - - Example Lab Manual: [AMR Africa 24](https://drive.google.com/file/d/11ZoiNcW36ZJ80YtqK269XRh3K4a577vS/view?usp=sharing) - - Example Lab Protocol: [Antimicrobial Susceptibility Testing](https://docs.google.com/document/d/1L6DxB2fvhtSmSnBN3dAKXfOG9jdG2kLQ/edit?usp=share_link&ouid=113316994580307529891&rtpof=true&sd=true) - -## Bioinformatics Manual Content Examples -- **Step-by-Step Instructions or Exercises:** This section, similar to the laboratory manuals, should provide comprehensive exercises focusing on bioinformatics. Each exercise should include: - - Clear learning objectives outlining what participants will achieve. - - A thorough description of the bioinformatics tools or software to be used. - - Instructions for data input, analysis, and interpretation of results. - - Examples of datasets to practice on and expected outcomes. - - - **Examples in Bioinformatics:** - - Example 1: [Helminths_2021, Module 6: Genome Variation](https://github.com/WCSCourses/Helminths_2021/blob/main/manuals/module_6_genome_variation/module_6_genome_variation.md) - - Example 2: [WWPG_2021, Task 2: Georeferencing Genomic Data](https://github.com/WCSCourses/WWPG_2021/blob/main/manuals/exercise_bacterial/Task2_georeferencing.pdf) - - Example 3: [ViralBioinfo_22, Module: Phylogenetics & Virus Typing](https://github.com/WCSCourses/ViralBioinfLAC2022/blob/main/Modules/Phylogeny_&_Virus_Typing_HandsOnEx.md) - - - For additional examples, please visit [WCSCourses GitHub](https://github.com/WCSCourses). - -## Converting Between Markdown and PDF -Markdown files can be converted to PDF format using Pandoc. For detailed instructions on how to perform this conversion, refer to the following tutorial: -- [Converting with Pandoc](https://github.com/WCSCourses/format_convert) - -### Helpful Links -1. [Using Markdown on GitHub](https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github) -2. [Formatting Markdown on GitHub](https://docs.github.com/en/github/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax) -3. [GitHub Markdown Cheatsheet](https://github.github.io/gfm/) -4. [Command Line GitHub Manual](https://cli.github.com/manual/) - ---- - -[Wellcome Connecting Science GitHub Home Page](https://github.com/WCSCourses)
-[Wellcome Connecting Science Courses & Conference Website](https://coursesandconferences.wellcomeconnectingscience.org/our-events/) diff --git a/course_modules_2023/Read_Alignment/NGS-2023-Alignment.pdf b/course_modules_2023/Read_Alignment/NGS-2023-Alignment.pdf deleted file mode 100644 index a92e1e1..0000000 Binary files a/course_modules_2023/Read_Alignment/NGS-2023-Alignment.pdf and /dev/null differ diff --git a/course_modules_2023/Read_Alignment/README.md b/course_modules_2023/Read_Alignment/README.md deleted file mode 100644 index 8b13789..0000000 --- a/course_modules_2023/Read_Alignment/README.md +++ /dev/null @@ -1 +0,0 @@ - diff --git a/course_modules_2023/Read_Alignment/read_alignment_practical.pdf b/course_modules_2023/Read_Alignment/read_alignment_practical.pdf deleted file mode 100644 index 943001d..0000000 Binary files a/course_modules_2023/Read_Alignment/read_alignment_practical.pdf and /dev/null differ diff --git a/course_modules_2023/Run_QC/README.md b/course_modules_2023/Run_QC/README.md deleted file mode 100644 index 8b13789..0000000 --- a/course_modules_2023/Run_QC/README.md +++ /dev/null @@ -1 +0,0 @@ - diff --git a/course_modules_2023/Unix_for_Bioinformatics/README.md b/course_modules_2023/Unix_for_Bioinformatics/README.md deleted file mode 100644 index 8b13789..0000000 --- a/course_modules_2023/Unix_for_Bioinformatics/README.md +++ /dev/null @@ -1 +0,0 @@ - diff --git a/course_modules_2023/Unix_for_Bioinformatics/linux_practical.pdf b/course_modules_2023/Unix_for_Bioinformatics/linux_practical.pdf deleted file mode 100644 index 6fcf7cd..0000000 Binary files a/course_modules_2023/Unix_for_Bioinformatics/linux_practical.pdf and /dev/null differ diff --git a/course_modules_2023/Unix_for_Bioinformatics/linux_slides.pdf b/course_modules_2023/Unix_for_Bioinformatics/linux_slides.pdf deleted file mode 100644 index 8c0f766..0000000 Binary files a/course_modules_2023/Unix_for_Bioinformatics/linux_slides.pdf and /dev/null differ diff --git a/course_modules_2023/Variant_Calling/README.md b/course_modules_2023/Variant_Calling/README.md deleted file mode 100644 index 8b13789..0000000 --- a/course_modules_2023/Variant_Calling/README.md +++ /dev/null @@ -1 +0,0 @@ - diff --git a/course_modules_2023/Variant_Calling/variant-calling-talk.pdf b/course_modules_2023/Variant_Calling/variant-calling-talk.pdf deleted file mode 100644 index ba66a15..0000000 Binary files a/course_modules_2023/Variant_Calling/variant-calling-talk.pdf and /dev/null differ diff --git a/course_modules_2023/Variant_Calling/variant_calling_practical.pdf b/course_modules_2023/Variant_Calling/variant_calling_practical.pdf deleted file mode 100644 index 165ab6b..0000000 Binary files a/course_modules_2023/Variant_Calling/variant_calling_practical.pdf and /dev/null differ diff --git a/course_modules_2023/module_base.md b/course_modules_2023/module_base.md deleted file mode 100644 index 8971e4a..0000000 --- a/course_modules_2023/module_base.md +++ /dev/null @@ -1,8 +0,0 @@ -# This is a base file to modify with your module content -## Please rename this md file to suit your module - -## Markdown guide is available -https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax - -## Example git -https://github.com/WCSCourses/WWPG_2022/blob/main/manuals/module_linux_scripting/module_linux_scripting.md