All Published Workflows

7 workflows that have been reviewed and published

mega-non-model-wgs-snakeflow
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Mega non-model WGS Snakeflow
public

public

There are two main changes: The genomics databases are now created directly from the gvcf sections. As a consequence, it ...
raw sequence reads Sequence clustering Score gatk rust-bio-tools snakemake-wrapper-utils BCFtools BWA FastQC gatk_realigner_target_creator MultiQC Pandas Picard SAMtools Snakemake Trimmomatic Variant Effect Predictor (VEP) tidyverse common matplotlib numpy seaborn vcfstats Genomics
Free
72
partial-ref-guided-workflow-gstacks-and-pops
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Partial Reference-Guided Workflow: Gstacks and Pops Analysis
public

public

workflow-partial-gstacks-populations These workflows are part of a set designed to work for RAD-seq data on the Galaxy platfo...
Map Sequence clustering Haplotype map Galaxy Stacks WorkflowHub Population genomics
Free
partial-ref-guided-workflow-bwa-mem-only
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Partial Reference-Guided Workflow: BWA-MEM Analysis
public

public

workflow-partial-bwa-mem These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using th...
Data Sequence clustering File format name Bwa-mem2 Galaxy MultiQC SAMtools Stacks WorkflowHub Population genomics
Free
partial-de-novo-workflow-c-s-g-pops-only
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Partial de novo workflow: cstacks-sstacks-gstacks-pops only
public

public

workflow-partial-cstacks-sstacks-gstacks These workflows are part of a set designed to work for RAD-seq data on the Galaxy pl...
Map Sequence clustering phenotype report Haplotype map Galaxy Stacks WorkflowHub Population genomics
Free
partial-de-novo-workflow-ustacks-only
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Partial de novo workflow: ustacks only
public

public

workflow-partial-ustacks-only These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, usi...
Data Sequence clustering Data Galaxy Stacks WorkflowHub Population genomics
Free
stacks-rad-seq-de-novo-workflow
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Stacks RAD-seq de novo workflow
public

public

workflow-denovo-stacks These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using the ...
Text data Sequence clustering File format name Galaxy Stacks WorkflowHub Population genomics
Free
stacks-rad-seq-reference-guided-workflow
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Stacks RAD-seq reference-guided workflow
public

public

workflow-ref-guided-stacks These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using ...
BAM Map Text data Sequence clustering Map data Bwa-mem2 Galaxy MultiQC SAMtools Stacks WorkflowHub Population genomics
Free