All Published Workflows

4 workflows that have been reviewed and published

assembly-annotation-pipeline
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Plant genome assembly and annotation pipeline using snakemake
public

public

This Snakemake pipeline aims for plant genome assembly with HiFi data and genome annotation with RNA-Seq/IsoSeq. Modified fro...
Genome index Annotation Map BEDTools BLAST fastp FastQC GFF3 Rebase gffread HISAT2 Minimap2 RepeatMasker RepeatModeler SAMtools Snakemake StringTie RNA-Seq
Free
20
hisss
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Snakemake workflow to download and/or align reads to targets and produce useful outputs.
public

public

A Snakemake workflow to download/align reads to targets and produce useful outputs. With hiss, you can: Download reads fo...
Sample annotation Mapping Map Bowtie 2 SAMtools Snakemake ggplot2 magrittr reshape2 Data identity and mapping
Free
10
eqtl-catalogue-qtlmap
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eQTL-Catalogue/qtlmap
public

public

eQTL-Catalogue/qtlmap Portable eQTL analysis and statistical fine mapping workflow used by the eQTL Catalogue eQTL-Cata...
Genotype and phenotype annotation ID Mapping Map csvtk plink2 tabix BCFtools QTL-ALL FastQTL QTL mapping
Free
23
workflow-of-biotranslator-comparative-analysis
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Workflow of BioTranslator Comparative Analysis
public

public

This workflow is based on the idea of comparing different gene sets through their semantic interpretation. In many cases, the...
Gene ID Pathway analysis Map BioTranslator Galaxy WorkflowHub Comparative genomics Gene expression
Free