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  • 13:26, 29 May 2026 Haars0011 talk contribs deleted page Soapdenovo2 r240 (content was: " '''[http://soap.genomics.org.cn/soapdenovo.html#intro2 SOAPdenovo2]''' is a popular genome assembler. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <source lang='tcl'>#%Module1.0####################################################################### ## SOAPdenovo2 r240 modulefile ## proc ModulesHelp { } { puts...", and the only contributor was "Megen002" (talk))
  • 13:26, 29 May 2026 Haars0011 talk contribs deleted page Snap (content was: "SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## snap 2013-11-29 modulefile ## proc ModulesHelp { } { puts stderr "\tAdds snap 2013-11-29 to your environment" } module-w...")
  • 13:26, 29 May 2026 Haars0011 talk contribs deleted page Services (content was: "Several additional services are also attached to Anunna's environment: * [https://wiki.anunna.wur.nl This wiki] is what you're looking at now. * [https://galaxy.anunna.wur.nl Galaxy] is a point-and-click friendly way of running genomics pipelines, which offloads the workload onto Anunna. * [https://notebook.anunna.wur.nl Jupyterhub] , the Jupyter notebook server, is a web-accessible environment for many languages. Primarily Python, includes R, octave, Julia etc.")
  • 13:25, 29 May 2026 Haars0011 talk contribs deleted page Samtools v0.1.19 (content was: "[http://samtools.sourceforge.net SAM Tools] provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## samtools 0.1.19 modulefile ## proc ModulesHelp { } { puts stderr "\tAdds sa...")
  • 13:25, 29 May 2026 Haars0011 talk contribs deleted page Samtools v0.1.12a (content was: "[http://samtools.sourceforge.net SAM Tools] provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## samtools 0.1.12a modulefile ## proc ModulesHelp { } { puts stderr "\tAdds s...")
  • 13:25, 29 May 2026 Haars0011 talk contribs deleted page SLURM Compare (content was: "=== Rosetta Stone of Workload Managers === PBS/Torque, Slurm, LSF, SGE and LoadLeveler [http://slurm.schedmd.com/rosetta.html Rosetta Stone] This table lists the most common command, environment variables, and job specification options used by the major workload management systems: PBS/Torque, Slurm, LSF, SGE and LoadLeveler. Each of these workload managers has unique features, but the most commonly used functionality is available in all of these environments as listed in the...")
  • 13:25, 29 May 2026 Haars0011 talk contribs deleted page RepeatModeler 1.0.7 (content was: "[http://www.repeatmasker.org/RepeatModeler.html RepeatModeler] is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build...")
  • 13:24, 29 May 2026 Haars0011 talk contribs deleted page RepeatMasker 4.0.3 (content was: "[http://www.repeatmasker.org RepeatMasker]RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (i.e. replace...", and the only contributor was "Megen002" (talk))
  • 13:24, 29 May 2026 Haars0011 talk contribs deleted page RAxML8.0.0 (content was: "'''[http://www.exelixis-lab.org RAxML]''' (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It can also be used for postanalyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0########################################...")
  • 13:24, 29 May 2026 Haars0011 talk contribs deleted page Quantitative genetics protocols ABG Chairgroup (content was: "* run_ASREML_with_SGE", and the only contributor was "Hjmegens" (talk))
  • 13:24, 29 May 2026 Haars0011 talk contribs deleted page Quantitative genetics (content was: "* Quantitative genetics Discussion Group: QDG * Quantitative genetics: topics * best practices, tips and workflows", and the only contributor was "Hjmegens" (talk))
  • 13:24, 29 May 2026 Haars0011 talk contribs deleted page Provean Sus scrofa (content was: "This page describes the procedure for mapping all known variants (batch of first 150 pigs, wild boar re-sequencing) at the ABGC. == Pre-requisites == From Variant Effect Predictor output, select only protein altering variants and sort by transcript: <source lang='bash'> cat outVEP_*.txt | awk '$11~/\//' | sed 's/:/\t/' | sort -k6 >prot_alt.txt </source> Protein models for Sus scrofa: /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/pig/Ensembl74/pep/Sus_scrofa.Ss...")
  • 13:23, 29 May 2026 Haars0011 talk contribs deleted page Provean 1.1.3 (content was: "[http://provean.jcvi.org/about.php PROVEAN] was developed to predict whether a protein sequence variation affects protein function. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## Provean 1.1.3 modulefile ## proc ModulesHelp { } { puts stderr "\tAdds Provean 1.1.3 to your environment" } module-whatis "Adds Provean 1.1.3 to y...")
  • 13:23, 29 May 2026 Haars0011 talk contribs deleted page Plink 1.9 (content was: "[https://www.cog-genomics.org/plink2/ PLINK] is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Development of the baseline PLINK toolset has resumed and beta testing for the next (1.90) release has now begun.The new release, by Chris Chang and colleagues, is a complete rewrite of the original code and represents a very significant improvement in overall speed and fu...")
  • 13:23, 29 May 2026 Haars0011 talk contribs deleted page Plink 1.07 (content was: "[http://pngu.mgh.harvard.edu/~purcell/plink/index.shtml PLINK] is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## plink 1.07 modulefile ## proc ModulesHelp { } { puts s...")
  • 13:22, 29 May 2026 Haars0011 talk contribs deleted page Muscle 3.8.31 (content was: "'''[http://www.drive5.com/muscle/ MUSCLE]''' is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes—only a handful of command-line optio...", and the only contributor was "Megen002" (talk))
  • 13:22, 29 May 2026 Haars0011 talk contribs deleted page Migration from ESG HPC (content was: " == Folders == home folder (200GB limit): /home/WUR/<user>/ lustre backup folder: /lustre/backup/WUR/ESG/<user>/ lustre no-backup folder: /lustre/nobackup/WUR/ESG/<user>/ /DATA folder /lustre/backup/WUR/ESG/data/ == Example of a job script == #!/bin/bash #SBATCH --comment=99999999 #SBATCH --time=1200 #SBATCH --mem=2048 #SBATCH --ntasks=1 #SBATCH --output=output_%j.txt #SBATCH --error=error_output_%j.txt #SBATCH --job-name="test slurm" #SBATCH --no...")
  • 13:20, 29 May 2026 Haars0011 talk contribs deleted page Maker protocols Pmajor (content was: "This page describes the various rounds of [http://www.yandell-lab.org/software/maker.html Maker]-based annotations for the [http://en.wikipedia.org/wiki/Parus_major ''Parus major'' (Great Tit)] genome. == Round 1 == === Rationale === For this round no P. major-based ESTs were available. Zebrafinch (T. guttata) is the closest relative for which a reasonably complete gene-model set is available. As a first pass, it was decided to let gene predictions be driven by ab-inititio pr...")
  • 13:20, 29 May 2026 Haars0011 talk contribs deleted page Maker 2.2.8 (content was: "Maker is a gene prediction/annotation pipeline. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## maker 2.28 modulefile ## proc ModulesHelp { } { puts stderr "\tAdds maker 2.28 to your environment" } module-whatis "Adds maker 2.28 to your environment" module load BLAST+/2.2.28 RepeatMasker/4.0.3 exonerate/2.2.0-x86_64 snap/20...")
  • 13:19, 29 May 2026 Haars0011 talk contribs deleted page Mailinglist (content was: "== Available mailling lists == In order to improve collaboration between Anunna users and to provide an easy to use platform in order to exchange ideas, Anunna has a public mailing list service available. More info about the software itself, mailman, can be found on this [http://www.list.org/ website]. All users are automatically added to the mailing list on registration, but if you're not, then subscribe to the [https://master1.anunna.wur.nl/mailman/listinfo/ Annuna's] maili...")
  • 13:19, 29 May 2026 Haars0011 talk contribs deleted page MAFFT 7.130 (content was: "'''[http://mafft.cbrc.jp/alignment/software/ MAFFT]''' is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0#####################################################################...")
  • 13:19, 29 May 2026 Haars0011 talk contribs deleted page Lx6 and Lx7 compute nodes (content was: "== HPC infrastructure== Schematic of bioinformatics infrastructure at ABGC. Lx5 is running Red Hat Enterprise Linux (RHEL) 6. Lx6 and Lx7 are running Ubuntu LTS 12.04. Jobs can be submitted with the Sun Grid Engine (SGE). A user account is needed to work on the machines. thumb|left|600px {{-}} * scomp1038 aka lx5...", and the only contributor was "Hjmegens" (talk))
  • 13:18, 29 May 2026 Haars0011 talk contribs deleted page Jellyfish 2.1.1 (content was: "'''[http://www.cbcb.umd.edu/software/jellyfish/ Jellyfish]''' is a fast, parallel k-mer counter for DNA. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## Jellyfish 2.1.1 modulefile ## proc ModulesHelp { } { puts stderr "\tAdds Jellyfish 2.1.1 to your environment" } module-whatis "Adds Jellyfish 2.1.1 to your environment" set...")
  • 13:18, 29 May 2026 Haars0011 talk contribs deleted page Installing WRF and WPS (content was: "==General config== The following setup works for WRF version 4.0! To install WRF download the WRF and WPS source code from http://www2.mmm.ucar.edu/wrf/users/download/get_source.html and untar into your directory load the following modules: * GCC OR INTEL * HDF5 * NETCDF * OpenMPI * JasPER Known good versions: * gcc: ** jasper/gcc/64/1.900.1 ** gcc/6.3.0 ** hdf5/gcc/64/1.10.1 ** netcdf/gcc/64/4.6.1 ** openmpi/gcc/64/3.1.1 ==WRF== Run ./configure and choose the (dmpar)...")
  • 13:17, 29 May 2026 Haars0011 talk contribs deleted page Hmmer 3.1 (content was: "[http://hmmer.janelia.org HMMER] is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <source lang='tcl'> #%...", and the only contributor was "Megen002" (talk))
  • 13:17, 29 May 2026 Haars0011 talk contribs deleted page Hadoop (content was: "Hadoop is another kind of architecture to promote writing code that can be executed in a parallel fashion. It's become more of an environment than a piece of software these days, as it typically contains: * HBase, flat table storage * Hive, a form of data warehousing * MapReduce, a style of coding to promote largely non-interacting workflows in order to leverage slow interconnects between workers * HDFS, a distributed filesystem between workers And many other components. This...")
  • 13:17, 29 May 2026 Haars0011 talk contribs deleted page Genomics Journal Club (content was: "Genomics Journal Club > How to choose your paper: We'd like to restrain a little the scope of the journal club, because it can very easily drift. Thus, we'd prefer if you present papers linked to Genomics, molecular biology or evolutionary biology. However, if you'd like to present a paper that you find particularly interesting but do not fall directly into these categor...", and the only contributor was "Hjmegens" (talk))
  • 13:17, 29 May 2026 Haars0011 talk contribs deleted page Genewise 2.2.3 (content was: " Compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## genewise 2.2.3-rc7 modulefile ## proc ModulesHelp { } { puts stderr "\tAdds genewise 2.2.3 to your environment" } module-whatis "Adds genewise 2.2.3 to your environment" set...")
  • 13:17, 29 May 2026 Haars0011 talk contribs deleted page Genetics and Genomics (content was: "The sphere of activity of genetics and genomics involves identifying the role of genetic factors in the functioning of farm animals and companion animals, as well as designing optimal breeding schemes for selection. The Animal Breeding & Genomics Centre (ABGC) works closely with the Department of Animal Sciences of Wageningen University. The ABGC has three key expertise are...", and the only contributor was "Hjmegens" (talk))
  • 13:16, 29 May 2026 Haars0011 talk contribs deleted page Geneid 1.4.4 (content was: "[http://genome.crg.es/software/geneid/ geneid] is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## geneid 1.4.4 modulefile ## proc ModulesHelp { } { puts stderr "\tAdds geneid v1.4.4 to your environment" } module-whatis "Adds gen...")
  • 13:16, 29 May 2026 Haars0011 talk contribs deleted page Fastq (content was: "'''FASTQ format''' is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are encoded with a single ASCII character for brevity. It was originally developed at the Wellcome Trust Sanger Institute to bundle a FASTA sequence and its quality data, but has recently become the ''de facto'' standard for storing the output o...")
  • 13:16, 29 May 2026 Haars0011 talk contribs deleted page Exonerate 2.2.0 (content was: "[https://www.ebi.ac.uk/~guy/exonerate/ Exonerate] is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <source lang='tcl'> #%Module1.0#######...", and the only contributor was "Megen002" (talk))
  • 13:16, 29 May 2026 Haars0011 talk contribs deleted page Cufflinks (content was: "'''[http://cufflinks.cbcb.umd.edu Cufflinks]''' assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support...", and the only contributor was "Megen002" (talk))
  • 13:16, 29 May 2026 Haars0011 talk contribs deleted page Computer cluster (content was: "The HPC infrastructure at the Animal Breeding and Genomics Centre is currently in a transition phase. Over the past years the main infrastructure consisted of the Lx6 and Lx7 compute nodes. As of December 2013 the new B4F cluster has become online is expected to replace the old infrastructure early 2014. The Lx6 and Lx7 comp...", and the only contributor was "Hjmegens" (talk))
  • 13:15, 29 May 2026 Haars0011 talk contribs deleted page Cegma 2.4 (content was: "CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virtually any eukaryotic genome. The strategy relies on a simple fact: some highly conserved proteins are encoded in essentially all eukaryotic genomes. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## cegma 2.4 mod...")
  • 13:15, 29 May 2026 Haars0011 talk contribs deleted page Canu (content was: "Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). Canu is a hierarchical assembly pipeline which runs in four steps: * Detect overlaps in high-noise sequences using MHAP * Generate corrected sequence consensus * Trim corrected sequences * Assemble trimmed corrected sequen...", and the only contributor was "Dawes001" (talk))
  • 13:13, 29 May 2026 Haars0011 talk contribs deleted page Bwa 7.5 (content was: "[http://en.wikipedia.org/wiki/Burrows-Wheeler_Aligner#Short-Read_Sequence_Alignment BWA] is a short read aligner designed by Heng Li and currently the most widely used aligner for re-sequencing analysis. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <source lang='tcl'> #%Module1.0#########################################...", and the only contributor was "Megen002" (talk))
  • 13:12, 29 May 2026 Haars0011 talk contribs deleted page Bwa 5.9 (content was: "[http://en.wikipedia.org/wiki/Burrows-Wheeler_Aligner#Short-Read_Sequence_Alignment BWA] is a short read aligner designed by Heng Li and currently the most widely used aligner for re-sequencing analysis. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <source lang='tcl'> #%Module1.0#########################################...", and the only contributor was "Megen002" (talk))
  • 13:12, 29 May 2026 Haars0011 talk contribs deleted page Bowtie2 v2.2.1 (content was: " '''[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]''' is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an...", and the only contributor was "Megen002" (talk))
  • 13:12, 29 May 2026 Haars0011 talk contribs deleted page Bowtie1 v1.0.0 (content was: "'''[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie]''' is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB f...", and the only contributor was "Megen002" (talk))
  • 13:12, 29 May 2026 Haars0011 talk contribs deleted page Blat v35 (content was: "'''[http://en.wikipedia.org/wiki/BLAT_(bioinformatics) BLAT]''' (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the Human Genome. == Module file == The module file can be found in this location: /cm/shared...", and the only contributor was "Megen002" (talk))
  • 13:12, 29 May 2026 Haars0011 talk contribs deleted page Bioinformatics topics at ABG Chairgroup (content was: "This page contains a list of research topics. * Pig ERC project * Porcine HapMap project", and the only contributor was "Hjmegens" (talk))
  • 13:11, 29 May 2026 Haars0011 talk contribs deleted page DE expression (content was: "=== Typical commands used for doing a DE expression study using Tophat (including Bowtie2 as aligner), Stringtie and Cuffdiff === Author: Martijn Derks * Samtools, Trimmomatic, Tophat, Bowtie2, Stringtie, Cufflinks need to be in PATH. * Use case in wintermoth. 12 samples (1 Egg, 1 Caterpillar, 3x3 Pupa, 1 Moth). ===Trim sequences for quality and adapters=== <source lang...", and the only contributor was "Derks047" (talk))
  • 13:11, 29 May 2026 Haars0011 talk contribs deleted page Issues asreml (content was: "Issues with ASReml on the HPC and possible solutions == Issue with the environment variable DISPLAY == '''Issue''' Some terminals for Windows (e.g., MobaXterm) set the environment variable DISPLAY to a specific value. This can cause issues with (some versions of) ASReml. '''Solution 1''' If you don't need a X11 server, you can disable it. '''Solution 2''' You can a...", and the only contributor was "Vande018" (talk))
  • 13:11, 29 May 2026 Haars0011 talk contribs deleted page Variant annotation tutorial (content was: "Code and tutorials for CIHEAM course. Variation annotation and function prediction sessions == Variant annotation == make a new folder to work in, and go there: <source lang='bash'> mkdir annotation_session cd annotation_session </source> Create an Env.Var. to the communal session directory that holds some of the files you need: <source lang='bash'> SESSIONDIR=/home/for...", and the only contributor was "Megen002" (talk))
  • 13:10, 29 May 2026 Haars0011 talk contribs deleted page RNA-seq analysis (content was: " === Typical commands used for analyzing RNA-seq with Tophat (including Bowtie2 as aligner).=== * Examples are RNA-seq (stranded) from pig aligned against the pig reference genome (''S. scrofa'' - 10.2) * Tophat, Bowtie2, Picard and GATK need to be in PATH or loaded as modules (e.g.: module load SHARED/bowtie/2-2.2.1; module load SHARED/tophat/2.0.11) * Bowtie2 index (made with bowtie2_build) of reference genome (need only to be made ones) * PCR duplicates removed with Picar...")
  • 13:10, 29 May 2026 Haars0011 talk contribs deleted page Calculate corrected theta from resequencing data (content was: "This procedure will estimate theta (nucleotide diversity) based on re-sequencing data. The method is describe in [http://www.biomedcentral.com/1471-2164/14/148 Esteve-Codina et al.] <source lang ='bash'> #!/bin/bash #SBATCH --time=10000 #SBATCH --mem=4000 #SBATCH --ntasks=1 #SBATCH --nodes=1 #SBATCH --constraint=4gpercpu #SBATCH --output=output_%j.txt #SBATCH --error=error_output_%j.txt #SBATCH --job-name=ngstheta module load samtools/0.1.19 VAR=`gunzip -c /lustre/nobackup/WU...")
  • 13:10, 29 May 2026 Haars0011 talk contribs deleted page Extract noncall snps from soy (content was: "== Extract the SNPs that are not called in Soy == From the <code>.ped</code> file, only the soy samples were extracted, and call rate calculated like this: <source lang='bash'> ./plink --file soy --out soy --missing-genotype N --freq --noweb </source> The output data looks like this: CHR SNP A1 A2 MAF NCHROBS 1 MARC0044150 0 0...", and the only contributor was "Megen002" (talk))
  • 13:10, 29 May 2026 Haars0011 talk contribs deleted page Command line tricks for manipulating fastq (content was: "== Extracting a sequence based on read name == <source lang='bash'> gunzip -c reads.fq.gz | sed -n '/readname/,+3 p' </source> == From BAM/SAM to fastq == <source lang='bash'> samtools view bamfile.bam | grep -v '^@' | awk '{print "@"$1"\n"$10"\n+\n"$11}' </source> == From fastq to fasta == <source lang='bash'> gunzip -c fastqfile.fq.gz | sed 's/^@/>/' | awk '{print;get...", and the only contributor was "Megen002" (talk))
  • 13:09, 29 May 2026 Haars0011 talk contribs deleted page Short read mapping pipeline pig (content was: "The latest short-read mapping pipeline for the pig project is based on a Python3 script that creates a shell script that can subsequently be executed from the command line or submitted to the cluster using SLURM. The latest version of the Python3 script can be found at [https://github.com/hjmegens/NGStools/blob/master/ABGC_mapping_v2.py GitHub]. The script requires to be executed using python3. == Prerequisites == === Data sources === * path to sequence archives...")
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