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• 11:50, 12 January 2026 Rasmus talk contribs created page File:Microbial genomics course22126 slide31-75 compressed.pdf
• 11:50, 12 January 2026 Rasmus talk contribs uploaded File:Microbial genomics course22126 slide31-75 compressed.pdf
• 11:34, 12 January 2026 Rasmus talk contribs created page File:Microbial genomics course22126 slide1-30 compressed.pdf
• 11:34, 12 January 2026 Rasmus talk contribs uploaded File:Microbial genomics course22126 slide1-30 compressed.pdf
• 09:37, 11 January 2026 Mick talk contribs created page Solution (Created page with "<hr> <h2>Answers</h2> <p><b>Marsupials Newick</b></p> <pre> myTree <- read.tree(text = "((Echidna,Platypus),(American_Opossums,(Monito_del_Monte,((((Koalas,Wombats),(Possums,(Kangaroos,Wallabies))),(((Bandicoots,Bilby),Marsupial_Mole),((Tasmanian_Devil,Tasmanian_Tiger),Numbats)))))));") </pre> <p><b>Q1.</b> The two trees contain the same information about relationships, but the rooted tree additionally contains information about the most recent common ancestor of...")
• 01:15, 10 January 2026 Rasmus talk contribs created page File:Slide pa distribution.png
• 01:15, 10 January 2026 Rasmus talk contribs uploaded File:Slide pa distribution.png
• 23:32, 9 January 2026 Rasmus talk contribs created page File:Nielsen et al 2025 Application of rapid Nanopore metagenomic cell-free DNA sequencing to diagnose bloodstream infections.pdf
• 23:32, 9 January 2026 Rasmus talk contribs uploaded File:Nielsen et al 2025 Application of rapid Nanopore metagenomic cell-free DNA sequencing to diagnose bloodstream infections.pdf
• 02:08, 9 January 2026 Rasmus talk contribs uploaded a new version of File:Full tree.png
• 02:07, 9 January 2026 Rasmus talk contribs uploaded a new version of File:STunknown removed tree.png
• 02:03, 9 January 2026 Rasmus talk contribs created page File:STunknown removed tree.png
• 02:03, 9 January 2026 Rasmus talk contribs uploaded File:STunknown removed tree.png
• 01:59, 9 January 2026 Rasmus talk contribs created page File:Full tree.png
• 01:59, 9 January 2026 Rasmus talk contribs uploaded File:Full tree.png
• 12:16, 8 January 2026 Rasmus talk contribs created page File:Spectrum.03295-24-s0001.docx
• 12:16, 8 January 2026 Rasmus talk contribs uploaded File:Spectrum.03295-24-s0001.docx
• 12:12, 7 January 2026 Mick talk contribs created page Exercise and answers (Created page with "<h2>Overview</h2> <p> In this mini-workshop you will familiarize yourself with <b>TADbit</b> (Serra et al., 2017): from FASTQ files to contact matrix and beyond. </p> <p> <b>A Primer into 3D Genomics: A Mini-Workshop</b><br> Juan Antonio Rodríguez, Globe Institute, University of Copenhagen<br> 9 January 2026, DTU </p> <hr> <h2>Outline of the exercises</h2> <ol> <li>Preprocess Hi-C FASTQ data</li> <li>Index reference genome</li> <li>Use TADbit to: <ol>...")
• 13:57, 6 January 2026 Rasmus talk contribs created page Microbial genomics exercise (Created page with " Dear course participants, In this exercise you will analyse microbial genome sequences using bioinformatics tools that are commonly used for microbial diagnostics and research. == Background == We imagine that we are employed at a hospital to provide diagnostics for patient care. The laboratory has sequenced genomic DNA from a clinical specimen. The sequence reads are stored in FASTQ files that are compressed with gzip: * X * Y Use the following command to read t...")
• 13:49, 6 January 2026 Rasmus talk contribs created page File:Gtdbtk.pdf
• 13:49, 6 January 2026 Rasmus talk contribs uploaded File:Gtdbtk.pdf
• 15:19, 12 December 2025 Rasmus talk contribs created page Exercise (Created page with "fefefeefefefefefe")
• 15:09, 12 December 2025 User account Rasmus talk contribs was created by WikiSysop talk contribs
• 11:03, 20 November 2025 Mick talk contribs created page Advanced UNIX and Pipes (Created page with "== Advanced UNIX and Pipes == This page covers standard input/output streams, redirection, pipes, file descriptors, and examples using Python scripts. These concepts are extremely useful in NGS analysis (e.g., chaining commands together, avoiding intermediate files, streaming FASTQ/BAM data, etc.). === stdout, stdin, stderr === Every UNIX command uses three data streams: * '''stdin''' (file descriptor 0) – input * '''stdout''' (file descriptor 1) – normal output...")
• 11:02, 20 November 2025 Mick talk contribs created page Basic UNIX notes (Created page with "=== Introduction to UNIX === UNIX refers to a family of multitasking, multi-user operating systems that originated from AT&T Unix (Bell Labs, 1969). Many modern operating systems are UNIX-like and inherit its core principles of stability, flexibility, and powerful command-line tools. Although UNIX may appear complex at first, it is essential in bioinformatics and NGS analysis. Most tools you will use in this course (and in real research) run exclusively on the command l...")
• 16:43, 19 November 2025 Mick talk contribs created page Unix Exercises (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: None |Next: Python Recap and Objects |} You did complete the Course preparation, right? Otherwise, all of this will fail. == Required course material for the lesson == PowerPoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_01-Unix.ppt Introduction to Unix] The videos are not entirely in sync with the updated PowerPoint. Video: [https:...")
• 10:23, 19 November 2025 Mick talk contribs created page Program 2026 (Created page with " '''NOTE: THIS PAGE IS UNDER CONSTRUCTION WITH A NEW TEACHER IN 2026''' '''REMEMBER TO BRING A LAPTOP FOR EXERCISES''' Lectures will be in person in building [https://maps.app.goo.gl/wH5EW199wrChCmWK7 341] in auditorium 23. <!-- Lectures and exercises will take place on Discord (https://discord.gg/FBb2edFW). Please register with your full name. Will use Discord for online classes and collaboration with your project partners. --> The course has two main parts, the...")
• 12:05, 25 August 2025 User account Mick talk contribs was created by WikiSysop talk contribs
• 14:26, 8 January 2025 Gabre talk contribs created page SNP calling exercise answers part 2 (Created page with " '''Q1''' First running: <pre> gatk VariantFiltration -V NA24694.vcf.gz -O NA24694_hf.vcf.gz -filter "DP < 10.0" --filter-name "DP" -filter "QUAL < 30.0" --filter-name "QUAL30" -filter "SOR > 3.0" --filter-name "SOR3" -filter "FS > 60.0" --filter-name "FS60" -filter "MQ < 40.0" --filter-name "MQ40" </pre> and <pre> bcftools view -H NA24694_hf.vcf.gz |grep -v PASS |wc -l </pre> Gives us 4005 sites. <pre> bcftools view -H --type=...")
• 17:28, 15 December 2024 Gabre talk contribs created page SNP calling exercise part 2 answers (Created page with "'''Q1''' First, running: <pre> tabix -f -p vcf NA24694.gvcf.gz </pre> then <pre> gatk --java-options "-Xmx10g" HaplotypeCaller -R /home/databases/references/human/GRCh38_full_analysis_set_plus_decoy_hla.fa -I /home/projects/22126_NGS/exercises/snp_calling/NA24694.bam -L chr20 -O NA24694.gvcf.gz --dbsnp /home/databases/databases/GRCh38/Homo_sapiens_assembly38.dbsnp138.vcf.gz -ERC GVCF </pre> <pre> gatk GenotypeGVCFs -R /home/databases/references/human/GRCh3...")
• 17:27, 15 December 2024 Gabre talk contribs created page SNP calling exercise part 1 answers (Created page with "'''Q1''' First, running: <pre> tabix -f -p vcf NA24694.gvcf.gz </pre> then <pre> gatk --java-options "-Xmx10g" HaplotypeCaller -R /home/databases/references/human/GRCh38_full_analysis_set_plus_decoy_hla.fa -I /home/projects/22126_NGS/exercises/snp_calling/NA24694.bam -L chr20 -O NA24694.gvcf.gz --dbsnp /home/databases/databases/GRCh38/Homo_sapiens_assembly38.dbsnp138.vcf.gz -ERC GVCF </pre> <pre> gatk GenotypeGVCFs -R /home/databases/references/human/GRCh3...")
• 18:20, 10 December 2024 Gabre talk contribs created page Unix pipes (Created page with "Welcome! This small guide contains a lot of information and examples that will help you as you start learning Linux. In addition to simple Linux commands, this tutorial also provides three Python scripts, that you can run and try out the concepts yourself. # Basic Unix Commands and Concepts This is where your journey begins! If you are new to Unix-based systems and also got used to Windows or MacOS, you really need a brief explanation of a few key commands and concept...")
• 16:06, 29 November 2024 Gabre talk contribs created page SNP calling exercise part 2 (Created page with " <H2> Filtering</H2> We saw that the data contains some calls of poor quality. Ideally, we do not want to carry over these calls into downstream analyses. We will explore how to filter out genotype data. <H3> Hard filtering </H3> A major downside of soft filtering is that does not apply for samples for which we do not have a good representation of the genetic diversity. An alternative is to do hard filtering meaning filtering the variants according to predetermined...")
• 15:35, 29 November 2024 Gabre talk contribs created page SNP calling exercise answers part 1 (Created page with "'''Q1''' First, running: <pre> tabix -f -p vcf NA24694.gvcf.gz </pre> then <pre> gatk --java-options "-Xmx10g" HaplotypeCaller -R /home/databases/references/human/GRCh38_full_analysis_set_plus_decoy_hla.fa -I /home/projects/22126_NGS/exercises/snp_calling/NA24694.bam -L chr20 -O NA24694.gvcf.gz --dbsnp /home/databases/databases/GRCh38/Homo_sapiens_assembly38.dbsnp138.vcf.gz -ERC GVCF </pre> <pre> gatk GenotypeGVCFs -R /home/databases/references/human/GRCh3...")