All Published Workflows

16 workflows that have been reviewed and published

adapter_benchmark
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Benchmarking adapter and quality trimming tools
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public

Original implementation by Brian Bushnell (2014): http://seqanswers.com/forums/showthread.php?t=42776 The following tools are...
Sample ID Sequencing quality control Quality control report BBMap Cutadapt fastp Pandas Snakemake Trimmomatic matplotlib Quality affairs
Free
9
skin_microbiome
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MAG Snakemake Workflow
public

public

Overview System Requirements Running pipeline License Citation This pipeline has t...
scp CheckM dRep Mash MetaWRAP SPAdes ggplot2 RColorBrewer tidyr gtdbtk Quality affairs
Free
37
captcr-snakemake
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Snakemake Workflow for Pughlab CaptCR Pipeline Automation
public

public

This repository is to automate the pughlab captcr pipeline using a snakemake workflow The pipeline consists of barcode extrac...
Snakemake Quality affairs
Free
11
cap-tcr
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Pughlab CaptCR Pipeline Automation with Snakemake
public

public

This repository is to automate the pughlab captcr pipeline using a snakemake workflow The pipeline consists of barcode extrac...
Snakemake Quality affairs
Free
11
cap-tcr
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Automated captcr-snakemake Pipeline: Barcode Extraction, MixCR, QC, and Clone Tracking
public

public

Author: [email protected] Orginal repo: https://github.com/arnavaz/cap-tcr This repository is to automate the pug...
Snakemake Quality affairs
Free
11
vr-startinggrant-2023
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This is a repository holding code to obtain preliminary results for the VR Starting Grant 2023.
public

public

This Snakemake workflow contains all the code necessary to reproduce the preliminary results from my application to VR Starti...
Data index Analysis Report plink2 tabix ucsc-liftover BCFtools BEDTools Pandas pLink Quant Snakemake broom coloc cowplot data.table dplyr fitdistrplus ggh4x ggplot2 ggrepel kableExtra knitr MASS showtext tidyr numpy Quality affairs
Free
175
telsvirus
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Data Cleaning and Quality Control Workflow for Viral Sequencing Data
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public

[ ] Make sure all required outputs are in the all_rule [ ] Convert RVHaplo viral accession to Viral Name (+ access...
Biopython Minimap2 Pandas Snakemake oschmod tqdm Quality affairs Sequence analysis
Free
21
detectmutations
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singularity & snakemake workflow to detect mutations with several tools to detect mutations
public

public

Sylvain Schmitt April 20, 2021 Installation Usage Get data Locally HPC Work...
raw sequence reads Sequence mutation and randomisation Alignment gatk BEDTools Biostrings BWA FastQC FreeBayes MultiQC QualiMap SAMtools Snakemake Trimmomatic vcfR tidyverse Quality affairs
Free
29
gbif-data-quality-check-and-filtering-workflow-feb
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GBIF data Quality check and filtering workflow
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public

This Galaxy-E workflow was made from the "Cleaning GBIF data for the use in biogeography" tutorial and allows to: Use...
Data Sequence contamination filtering Map data Galaxy GBIF WorkflowHub Quality affairs
Free
air-quality-prediction-prototype
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Air Quality Prediction Prototype
public

public

A prototype implementation of the Air Quality Prediction pipeline in Galaxy, using CWL tools.
CWL Training Galaxy WorkflowHub Quality affairs
Free
longread-quality-control-and-filtering
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LongRead Quality Control and Filtering Workflow for Accurate Taxonomic Classification and Enhanced Data Quality
public

public

NanoPlot (read quality control) before and after filtering Filtlong (read trimming) Kraken2 taxonomic read classificati...
CWL Sequencing quality control Filtlong kraken2 Krona Minimap2 NanoPlot SAMtools Quality affairs
Free
7
workflow-for-illumina-quality-control-and-filterin
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Illumina Quality Control and Filtering Workflow for High-Quality Data Processing and Taxonomic Classification
public

public

Multiple paired datasets will be merged into single paired dataset. FastQC on raw data files fastp for read quality t...
CWL Sequencing quality control BBMap fastp FastQC Filtlong kraken2 Krona Minimap2 NanoPlot SAMtools Quality affairs Sequence analysis
Free
11