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# Demo de-novo assembly workflow

This workflow assembles short reads by running the obsolete Velvet assembler. It performs the same assembly on every sample with different k-mer length settings, and reports the longest contig in each case.

Type: Snakemake

Creators: None

Submitter: Chloe Hui

Demo assembly workflow

Demo de-novo assembly workflow

This workflow assembles short reads by running the obsolete Velvet assembler. It performs the same assembly on every sample with different k-mer length settings, and reports the longest contig in each case.

Type: Snakemake

Creators: Timothy Booth, BioFAIR

Submitter: Tim Booth

CUT&RUN GTN

CUT&RUN data analysis workflow. It uses fastQC, trim adapters with Trim Galore!, map with Bowtie2, filter the BAM and mark duplicates. Peaks are called with MACS2 and peaks from both replicates are intersected and then intersected to the ChIP peaks. Finally MEME ChIP is run to get the motifs.

Associated Tutorial

This workflows is part of the tutorial CUT&RUN data analysis, ...

Type: Galaxy

Creators: None

Submitter: Helena Rasche

QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN - subworkflows

Reference-based RNA-Seq data analysis

Associated Tutorial

This workflows is part of the tutorial Reference-based RNA-Seq data analysis, available in the GTN

Features

Type: Galaxy

Creators: None

Submitter: Helena Rasche

QC + Mapping + Counting (single+paired) - Ref Based RNA Seq - Transcriptomics - GTN

Reference-based RNA-Seq data analysis

Associated Tutorial

This workflows is part of the tutorial Reference-based RNA-Seq data analysis, available in the GTN

Features

Thanks to...

Workflow Author(s): Bérénice Batut, ...

Type: Galaxy

Creators: None

Submitter: Helena Rasche

Gigascience_Indels_SAV_non-reference_demonstration_STS26T-Gent_Workflow

Generating non-reference protein database for FragPipe discovery

Associated Tutorial

This workflows is part of the tutorial Neoantigen 2: Non-Reference-Database-Generation, available in the GTN

Features

Type: Galaxy

Creators: None

Submitter: Helena Rasche

Understanding Barcodes

Associated Tutorial

This workflows is part of the tutorial Understanding Barcodes, available in the GTN

Features

Type: Galaxy

Creators: None

Submitter: Helena Rasche

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