Workflows

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836 Workflows visible to you, out of a total of 912
nf-core/nascent

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Type: Nextflow

Creators: Ignacio Tripodi, Margaret Gruca

Submitter: WorkflowHub Bot

Clonal population analysis for TracerX study
Stable

The Galaxy workflow for clonal population analysis was designed to process patient mutation data extracted from cBioPortal, specifically using the TracerX study as an example. This workflow, part of the deliverable D3.2 for EOSC4Cancer developed at UiO, begins with a raw patient mutation table from cBioPortal, where modifications and formatting occur to prepare the data for analysis. Some data, notably the copy number alterations (referred to as "All_CN"), were manually uploaded to Galaxy to ...

Type: Galaxy

Creator: Jeanne Chèneby

Submitter: Jeanne Chèneby

DOI: 10.48546/workflowhub.workflow.1355.1

Photometric Redshift Estimation for Candidate Optical Counterparts of Astronomical Sources Extracted from Texts
Work-in-progress
No description specified

Type: Galaxy

Creators: None

Submitter: Andrei Variu

PVGA

PVGA is a powerful virus-focused assembler that does both assembly and polishing. For virus genomes, small changes will lead to significant differences in terms of viral function and pathogenicity. Thus, for virus-focused assemblers, high-accuracy results are crucial. Our approach heavily depends on the input reads as evidence to produce the reported genome. It first adopts a reference genome to start with. We then align all the reads against the reference genome to get an alignment graph. After ...

Type: Python

Creator: Zhi Song

Submitter: Zhi Song

DOI: 10.48546/workflowhub.workflow.1305.1

Assembly-Hifi-only-VGP3/main

Generate a genome assembly based on PacBio HiFi reads. Part of the VGP suite, it needs to be run after the VGP1 k-mer profiling workflow. The assembly contigs are built using HiFiasm, and the workflow generates assembly statistics, BUSCO reports, Merqury plots, and the contigs in fasta and GFA formats.

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Purge-duplicates-one-haplotype-VGP6b/main

Purge contigs marked as duplicates by purge_dups in a single haplotype (could be haplotypic duplication or overlap duplication). If you think the purged contigs might belong to the other haplotype, use the workflow VGP6 instead. This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5).

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Scaffolding-HiC-VGP8/main

This workflow performs the scaffolding of a genome assembly using HiC data with YAHS. Can be used on any assembly with Hi-C data, and the assembly in the gfa format. You can generate a gfa from a fasta using the gfastat tool. Part of the VGP set of workflows, it is meant to be run after the contigging (workflows 3,4, or 5), optional purging step (Workflow 6 or 6b), and an optionnal scaffolding with Bionano data (Workflow 7). This workflow includes QC with Assembly statistics, Busco, and Hi-C maps. ...

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

Assembly-Hifi-Trio-phasing-VGP5/main

Generate phased assembly based on PacBio HiFi reads and parental Illumina data for phasing. Part of the VGP workflow suite, it needs to be run after the Trio k-mer Profiling workflow VGP2. This workflow uses HiFiasm for contigging, and generates assembly statistics, BUSCO reports, Merqury plots, and the genome assembly contigs in fasta and GFA format.

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

nf-core/airrflow

GitHub Actions CI Status GitHub Actions Linting Status AWS CI ...

Type: Nextflow

Creators: Gisela Gabernet, Simon Heumos, Alexander Peltzer

Submitter: WorkflowHub Bot

mags-building/main

This workflow constructs Metagenome-Assembled Genomes (MAGs) using SPAdes or MEGAHIT as assemblers, followed by binning with four different tools and refinement using Binette. The resulting MAGs are dereplicated across the entire input sample set, then annotated and evaluated for quality. You can provide pooled reads (for co-assembly/binning), individual read sets, or a combination of both. The input samples must consist of the original reads, which are used for abundance estimation. In all cases, ...

Type: Galaxy

Creators: Bérénice Batut, Paul Zierep, Mina Hojat Ansari, Patrick Bühler, Santino Faack

Submitter: WorkflowHub Bot

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