Results for "pipeline"
Users
About me: ...f bioinformatics and computational biology, I mainly focus on chromosomal breakpoint and amniotes evolution. I (We) develop certain computational pipeline, and algorithms to harness th...68 days ago
- Skills: ChIP-seq pipeline tools
3514 days ago
- +3 more Users
Blogs
Five points for bioinformatics software/tools
...n view all of the parts of the program and see the logical flow of the pipeline. In addition, open source mak...ource programs to deal with cutting-edge problems or to customize your pipeline. Apart from your computa...3696 days ago
List of bioinformatics workflow management tools !
...scripting language for working with big data pipelines in computer systems of diffe...pe – A small language for defining pipeline stages and linking them toget...that simplifies writing parallel and scalable pipelines in a portable manner. [ ...1131 days ago
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Bookmarks
Next Generation Sequencing (NGS) Tutorials
...========================== NGS data analysis pipelines Detecting and annotating genetic variations using the HugeSeq pipeline DOI: 10.1038/nbt.2134...34/abstract WEP: a high-performance analysis pipeline for whole-exome data htt...3476 days ago
shovill: Assemble bacterial isolate genomes from Illumina paired-end reads
Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports...1208 days ago
- +113 more Bookmarks
Discussion topics
Does anyone have Nanopore latest updates?
...platform technology uses nanopores to analyse single molecules including DNA/RNA and proteins. With a broad patent portfolio, the Oxford Nanopore pipeline includes biological nanopores...3802 days ago
Pages
Genome Assembly Tools and Software - PART2 !!
...be easily inserted into an existing assembly pipeline. This modular design will fos...MetAMOS 1.5rc3 – Metagenomic Assembly pipeline for AMOSMetAMOS is an op...Microbial Genome AssemblyBugBuilder is a pipeline for the automated assembly an...2675 days ago
Awesome perl frameworks, libraries and software - PART 2
...script to backup qemu machines by Daniel Berteaud daniel@firewall-services.com Starlink/ORAC-DR - The ORAC-DR astronomy data reduction pipeline soh335/p5-Data-Wheren -...2483 days ago
Top-level pages
Most Commonly used Awk by Bioinformatician
...ace delimited data. Although you can achieve all its functionality with Perl, awk is simpler in many practical cases. Why awk? You can replace a pipeline of 'stuff | grep | sed | cut....3901 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...010. Full Text Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads....al, Nature Methods 7:909-912, 2010 Full Text [describes Trans-ABySS, a pipeline to use the ABySS parallel ass...3768 days ago
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Wire posts
News
- ...eover, phylomeDB provides genome-wide orthology and paralogy predictions which are based on the analysis of the phylogenetic trees. The automated pipeline used to reconstruct trees aim...
3908 days ago
Webinar on Streamlining large scale analysis using the Strand NGS Pipeline Manager on 24 Feb 2016
...scale NGS data analysis using the Strand NGS Pipeline Manager on 24 Feb 2016 Abstr...by a workflow-specific analysis section. The pipeline functionality in Strand NGS a...this webinar we will discuss the pre-packaged pipelines present in Strand NGS. The p...3001 days ago
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Opportunity posts
Structural polymorphism analysis from NGS data
...f repetitiveness of complex genomes. The tools will be integrated into pipelines and made available to end-us...mental designs in order to ensure compliance of produced datasets with pipelines requirements. He/she will be...3938 days ago
Software engineer/Computational Biologist - Equinome Ltd., Dublin, Ireland
...of Thoroughbred racehorses. Since its launch in 2010, Equinome has successfully commercialised three performance-related genetic tests, with a pipeline of further genetic tests in d...3519 days ago
- +13 more Opportunity posts
Bio-Scripts
Mapping with BWA-mem or BWA-sampe in one go with python script !
...integer specifying how many threads BWA-mem should use. --nomem can be specified to the above call to use BWA-sampe as the paired read alignment pipeline. https://github.com/ksahli...2113 days ago
- ...teration1.fa" echo "[REAPR pipeline] Running preprocess" echo "/..../ 01.stats" echo "[REAPR pipeline] Running fcdrate" /home/urbe..."Running reapr version 1.0.18 pipeline:" echo "/home/urbe/Tools/Rea..._____________________ test pipeline " reapr pipeline Wadine...
2088 days ago
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Tryst
Tryst with a Bioinformatician # Dr Altan Kara
...s / ten years? For my current research, I would like to design a pipeline to automatically integrate an...target discovery. In addition to this, I also like to develop another pipeline for prokaryotic TCS protein s...2351 days ago
Groups
...ls2) dietary intakes in observational studies3) explaining the biological effects of the diet4) characterizing a specific genotype or phenotype Pipeline of Metabolomics study: http:...3695 days ago
Tags
Basic Structure of Snakemake Pipeline Run !
/user/snakemake-demo$ ls config.json data envs scripts slurm-240702.out Snakefile data = mock data for the snakefile to use Snakefile = name of the snakemake “formula” file Note: The default file that snakemake looks for in the current working directory is the Snakefile. ...Tags: Snakemake, Pipeline, Flow, Learn
923 days ago
Illumina based assembly pipeline steps !
Illumina Merge re-sequenced FastQ files (cat) Read QC (FastQC) Adapter trimming (fastp) Removal of host reads (Kraken 2; optional) Variant calling Read alignment (Bowtie 2) Sort and index alignments (SAMtools) Primer sequence removal (iVar; amplicon data only) Duplicate read marking (p...Tags: assembly, pipeline, genome, illumina
866 days ago
Comments
Comment on "REAPR: a universal tool for genome assembly evaluation"
...t;_smalt.bam. This should take about twenty minutes. Finally we can use the smalt mapping, and the perfect mapping to run the reapr pipeline. Run reapr pipeline to get help on how to ru...1326 days ago
Comment on "Coronavirus Resources !"
SARS-CoV-2 SNP Calling pipeline https://github.com/DamienFr/CoV-homoplasy1448 days ago
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