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• 13:08, 29 May 2026 Haars0011 talk contribs deleted page Making slices from BAM files (content was: "This article describes how to automate the creation of slices from a collection of BAM files. This procedure assumes that all BAM files are together in a single folder. == Variable that points to the collection of bam files == First, make a variable BAMDIR that holds the path to the BAM files: <source lang='bash'> BAMDIR='/shared/Sus/BAM_files_hjm_newbuild10_2/' </source>...", and the only contributor was "Hjmegens" (talk))
• 13:08, 29 May 2026 Haars0011 talk contribs deleted page Convert fastq to fasta (content was: "Converting fasq to fasta can sometimes be useful. Here a simple perl script is described that can do this. The script works on a stream, and will output to STDOUT. Optional is filtering for reads that have a certain minimum length Example for invoking the script, assuming the script is named fastq_to_fasta.pl: <source lang='bash'> gunzip -c fastqfile.fq.gz | perl fastq_to_...", and the only contributor was "Hjmegens" (talk))
• 13:07, 29 May 2026 Haars0011 talk contribs deleted page Mapping reads with Mosaik (content was: "Within the Pig ERC project we have several mapping strategies. This article describes the mapping procedure using Mosaik for paired-end mapping to the reference assembly. == Prerequisites == === input reads === The mapping procedure requires paired end reads in fastq format. For the current procedure quality-trimmed reads are used. Forward and reverse reads should be in tw...", and the only contributor was "Hjmegens" (talk))
• 13:07, 29 May 2026 Haars0011 talk contribs deleted page Bioinformatics protocols ABG Chairgroup (content was: "This page is intended as a portal to pages concerning best practices, workflows and pipelines, and other protocols (including scripts). == A list of tutorials, workflows, and recipes == * Mapping Illumina GA2/HiSeq reads to the Sus scrofa genome assembly * A Perl script to convert fastq to fasta file format * Setup Printers on Ubuntu Machines * Mapping Pair-end reads with Stampy * making_slices_from_BAM_fil...")
• 13:07, 29 May 2026 Haars0011 talk contribs deleted page Bedtools2.18 (content was: "Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect t...")
• 13:07, 29 May 2026 Haars0011 talk contribs deleted page BLAST (content was: "'''B'''asic '''L'''ocal '''A'''lignment '''S'''earch '''T'''ool, or '''[http://en.wikipedia.org/wiki/BLAST BLAST]''', is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of s...", and the only contributor was "Megen002" (talk))
• 13:07, 29 May 2026 Haars0011 talk contribs deleted page BCPlatforms (content was: "{| class=wikitable | Issue || Originating contact person || Person handling issue || Comments |- | Test Issue || Me || You ja dat zal wel een problem kunnen zijn . zeker als ik het veel tekst geef || A test issue. |- | Test Issue 2 || |}")
• 13:06, 29 May 2026 Haars0011 talk contribs deleted page BCM on Anunna (content was: "Computing clusters are usually managed by [http://en.wikipedia.org/wiki/Cluster_manager cluster managing software]. Anunna uses the cluster management sofware from [http://www.brightcomputing.com Bright ]. BCM is currently is a popular choice for compute clusters of any size, including some very large ones. Bright is a spin-off from [http://www.clustervision.com ClusterVision], the company that aided in implementing the cluster. Furthermore, ClusterVision and [http://www.cluste...")
• 13:06, 29 May 2026 Haars0011 talk contribs deleted page BCData (content was: "This page contains information about BCData", and the only contributor was "Lith010" (talk))
• 13:05, 29 May 2026 Haars0011 talk contribs deleted page Augustus 2.7 (content was: ""AUGUSTUS is a gene prediction program for eukaryotes genomic sequences. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments." == Module file == The module file can be...", and the only contributor was "Megen002" (talk))
• 13:05, 29 May 2026 Haars0011 talk contribs deleted page Assembly & Annotation (content was: "=== Protocol with typical commands used for de novo assembly and annotation === ''Author:'' Martijn Derks ''All script referred to in this protocol can be found here:'' /home/WUR/derks047/BifDev/derks047 * Software * Preprocessing * Assembly * Assembly validation * Annotation * Submission * Visualization === Software === List of tools described in this protocol [http:...", and the only contributor was "Derks047" (talk))
• 13:05, 29 May 2026 Haars0011 talk contribs deleted page Assemble mitochondrial genomes from short read data (content was: "A simple procedure for assembling mitochondrial genomes based on whole-genome re-sequencing data. The first step is to extract reads from the sequence library based on a closely related entirely assembled genome (e.g., for pig, the MT genome as present in the genome build, but could also be of a related species). The genome is then assembled using SOAPdenovo. * a reference genome of a closely related population or species. * a bowtie2 index (make with bowtie2_build) * a blasta...")
• 13:05, 29 May 2026 Haars0011 talk contribs deleted page Animal Breeding and Genetics (content was: "The [http://www.abg.wur.nl/UK/ Animal Breeding and Genetics] chair group provides education and generates knowledge on the role and sustainable use of genetic variation in animals. The Animal Breeding and Genetics group contributes to our quality of life by providing knowledge to support the adequate supply of safe and healthy food of animal origin, and to enhance the healt...", and the only contributor was "Hjmegens" (talk))
• 13:05, 29 May 2026 Haars0011 talk contribs deleted page Allpathslg 51910 (content was: " '''[http://www.broadinstitute.org/software/allpaths-lg/blog/ ALLPATHS-LG]''' is a popular genome assembler. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## maker ALLPATHS-LG (51910 modulefile ## proc ModulesHelp { } { puts stderr "\tAdds ALLPATHS-LG (51910) to your environment" } module-whatis "Adds ALLPATHS-LG (51910) to...")
• 13:04, 29 May 2026 Haars0011 talk contribs deleted page Allpathslg 48961 (content was: " '''[http://www.broadinstitute.org/software/allpaths-lg/blog/ ALLPATHS-LG]''' is a popular genome assembler. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## maker ALLPATHS-LG (48961 modulefile ## proc ModulesHelp { } { puts stderr "\tAdds ALLPATHS-LG (48961) to your environment" } module-whatis "Adds ALLPATHS-LG (48961) to...")
• 13:03, 29 May 2026 Haars0011 talk contribs deleted page About ABGC (content was: "The Animal Breeding and Genomics Centre is a merger of the Animal Breeding & Genetics chair group, of the [http://www.wageningenuniversity.nl/UK/about/organisation/Chair%20groups/animal/ Animal Sciences Group], Wageningen University, and the Genetics and Genomics cluster of the WUR [http://www.livestockresearch.wur.nl/UK/ Livestock Research] Centre. The ABGC has three key...", and the only contributor was "Hjmegens" (talk))
• 13:03, 29 May 2026 Haars0011 talk contribs deleted page ANGSD 0.614 (content was: "[http://popgen.dk/wiki/index.php/ANGSD ANGSD] ANGSD is a software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium dep...", and the only contributor was "Herre011" (talk))
• 13:03, 29 May 2026 Haars0011 talk contribs deleted page ABGSA (content was: "== Rationale of the ABGSA == == Description of the layout == == Metadata database == Metadatabase name is ABGSAschema +-----------------------+ | Tables_in_ABGSAschema | +-----------------------+ | ABGSAschema_main | | filesize | | fqfile_attributes | | gc_cont | +-----------------------+ The most recent mysqldump file...", and the only contributor was "Hjmegens" (talk))
• 13:02, 29 May 2026 Haars0011 talk contribs deleted page ABGC secretariat (content was: "== Animal Breeding and Genetics Chair Group == <pre> Visiting Address Zodiac building number 122 De Elst 1 6708 WD, Wageningen Telefax: +31 317 483929 office.abg@wur.nl </pre> == Genetics and Genomics Research Cluster == ===Headquarters Lelystad:=== <pre> Visiting address Edelhertweg 15 8219 PH Lelystad Postal address P.O. Box 65 8200 AB Lelystad tel: +31 320 238 238 fa...", and the only contributor was "Hjmegens" (talk))
• 13:02, 29 May 2026 Haars0011 talk contribs deleted page ABGC lab (content was: "* protocols", and the only contributor was "Hjmegens" (talk))
• 13:02, 29 May 2026 Haars0011 talk contribs deleted page ABGC bioinformatics (content was: "The ABGC has several shared bioinformatics facilities. == Bioinformatics at the Animal Breeding and Genetics chairgroup == * Monday Genome Meeting * Bioinformatics: topics * best practices, tips and workflows == Bioinformatics at the Genetics and Genom...", and the only contributor was "Hjmegens" (talk))
• 13:01, 29 May 2026 Haars0011 talk contribs deleted page 1000Bulls mapping pipeline at ABGC (content was: "The 1000 Bulls mapping pipeline as currently implemented at ABGC is an extension of a generic pipeline developed for pig at ABGC. Modifications include use of bwa 5.9 in stead of later versions, as per the requirements of the 1000 Bulls consortium. Furthermore, the script will automate setting metadata in the BAM files such as including the official 1000 Bulls Ids of the individual cows. Another modification is the use of an sqlite-based database that holds some the metadata re...")
• 13:00, 29 May 2026 Haars0011 talk contribs deleted page AsAn (content before blanking was: "=== Protocol with typical commands used for de novo assembly and annotation === * Preprocessing * Assembly * Annotation * Submission * Visualization === Preprocessing === === Assembly === === Annotation === === Functional annotation === === Submission === === Other types of analysis ===")
• 12:50, 29 May 2026 Haars0011 talk contribs deleted page Convert between MediaWiki and other formats (content was: "There are various programs that can convert to and from MediaWiki format, as used in this Wiki, and other formats. This page lists some of them and provides explanation of how to use them. == Pandoc == [http://johnmacfarlane.net/pandoc/demos.html Pandoc] is an open source tool that can convert between different markup styles and languages. There is a [http://johnmacfarlane.net/pandoc/try/ web version of Pandoc] but that seems limited to small documents only. There's also a C...")
• 12:48, 29 May 2026 Haars0011 talk contribs deleted page New page (content was: "Now here is some stuff", and the only contributor was "Megen002" (talk))
• 12:33, 29 May 2026 Haars0011 talk contribs changed group membership for Itter003: granted bureaucrat and administrator (Admins should be admin)
• 12:33, 29 May 2026 Haars0011 talk contribs changed group membership for Honfi001: granted bureaucrat and administrator (Admins should be admin)
• 12:32, 29 May 2026 Haars0011 talk contribs changed group membership for Prins0891: granted bureaucrat and administrator (Admins should be admin)
• 12:16, 18 May 2026 User account Cheng044 talk contribs was created automatically
• 12:44, 14 April 2026 Prins0891 talk contribs created page Support (Created page with "Support")
• 13:17, 31 March 2026 User account Bosse04 talk contribs was created automatically
• 14:39, 27 March 2026 Haars0011 talk contribs created page File:Desktop extended form.png
• 14:39, 27 March 2026 Haars0011 talk contribs uploaded File:Desktop extended form.png
• 14:37, 27 March 2026 Haars0011 talk contribs created page File:Minimal desktop form.png
• 14:37, 27 March 2026 Haars0011 talk contribs uploaded File:Minimal desktop form.png
• 09:42, 25 March 2026 Honfi001 talk contribs created page Tutorials/Apptainer-GPUs (Created page with "= Running Apptainer with GPUs = Apptainer can pass through GPU hardware from the host into a container, allowing you to run GPU-accelerated workloads (such as deep learning inference or training) inside a fully contained environment. This page covers how to use both NVIDIA and AMD GPUs on the Anunna cluster. '''Important:''' Before you begin, make sure the following are in place: * Your <code>.sif</code> image files should be stored on '''Lustre''' (e.g. in your scrat...")
• 09:18, 25 March 2026 Honfi001 talk contribs created page Tutorials/Apptainer-Introduction (Created page with "= Introduction to Apptainer = == What is Apptainer? == Apptainer (formerly known as Singularity) is a container platform designed for High Performance Computing (HPC) environments. If you have heard of Docker, Apptainer solves a similar problem — it lets you package an application together with all of its dependencies (libraries, tools, configuration) into a single portable unit called a '''container'''. The key difference is that Apptainer was built from the ground...")
• 14:09, 24 March 2026 User account Breet005 talk contribs was created automatically
• 13:07, 24 March 2026 User account Loon053 talk contribs was created automatically
• 11:57, 23 March 2026 User account Krijg026 talk contribs was created automatically
• 14:24, 17 March 2026 Prins0891 talk contribs created page File:Screenshot from 2026-03-17 15-24-40.png
• 14:24, 17 March 2026 Prins0891 talk contribs uploaded File:Screenshot from 2026-03-17 15-24-40.png
• 14:22, 17 March 2026 Prins0891 talk contribs created page File:Screenshot from 2026-03-17 15-21-49.png
• 14:22, 17 March 2026 Prins0891 talk contribs uploaded File:Screenshot from 2026-03-17 15-21-49.png
• 14:21, 17 March 2026 Prins0891 talk contribs created page File:Screenshot from 2026-03-17 15-20-58.png
• 14:21, 17 March 2026 Prins0891 talk contribs uploaded File:Screenshot from 2026-03-17 15-20-58.png
• 14:20, 17 March 2026 Prins0891 talk contribs created page File:Screenshot from 2026-03-17 15-20-23.png
• 14:20, 17 March 2026 Prins0891 talk contribs uploaded File:Screenshot from 2026-03-17 15-20-23.png
• 14:20, 17 March 2026 Prins0891 talk contribs created page File:Screenshot from 2026-03-17 15-19-46.png
• 14:20, 17 March 2026 Prins0891 talk contribs uploaded File:Screenshot from 2026-03-17 15-19-46.png