Workflows

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1217 Workflows visible to you, out of a total of 1301
Joon-Klaps/viralgenie

A bioinformatics best-practice analysis pipeline for reconstructing consensus genomes and to identify intra-host variants from metagenomic sequencing data or enriched based sequencing data like hybrid capture.

Type: Nextflow

Creators: Joon-Klaps , Joon-Klaps

Submitter: WorkflowHub Bot

nf-core/pixelator

GitHub Actions CI Status GitHub Actions Linting Status AWS CI [![Cite ...

Type: Nextflow

Creator: Pixelgen Technologies AB

Submitter: WorkflowHub Bot

ERGA Profiling Long Reads v2505 (WF1)
Stable

The workflow takes a (trimmed) Long reads collection, runs Meryl to create a K-mer database, Genomescope2 to estimate genome properties and Smudgeplot to estimate ploidy (optional). The main results are K-mer database and genome profiling plots, tables, and values useful for downstream analysis. Default K-mer length and ploidy for Genomescope are 31 and 2, respectively.

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

DOI: 10.48546/workflowhub.workflow.603.1

Workflow 3D relion (tilted experiments variation)

Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using Relion.

Type: Scipion

Creators: None

Submitter: Daniel Marchan

Workflow 3D relion

Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using Relion.

Type: Scipion

Creators: None

Submitter: Daniel Marchan

Workflow 3D cryosparc (tilted experiments variation)

Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using CryoSPARC.

Adapting to Tilted Samples

To process tilted experiments, use ”tilted” templates. These are modified workflows tailored to handle ...

Type: Scipion

Creators: None

Submitter: Daniel Marchan

Workflow 3D cryosparc

Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using CryoSPARC.

Type: Scipion

Creators: None

Submitter: Daniel Marchan

Workflow 2D relion (tilted experiments variation)

Automated image processing from movies to 2D classes. Includes CTF estimation, quality filters, box size estimation, training a data-specific picking model, and three 2D classification jobs (25k, 50k, and 100k particles) using Relion.

Adapting to Tilted Samples

To process tilted experiments, use ”tilted” templates. These are modified workflows tailored to handle high drift and lower resolution commonly observed in tilted samples. Key adjustments include:

  • Motion Correction Filters: Max ...

Type: Scipion

Creators: None

Submitter: Daniel Marchan

Workflow 2D relion

Automated image processing from movies to 2D classes. Includes CTF estimation, quality filters, box size estimation, training a data-specific picking model, and three 2D classification jobs (25k, 50k, and 100k particles) using Relion.

Type: Scipion

Creators: None

Submitter: Daniel Marchan

Workflow 2D cryosparc (tilted experiments variation)

Automated image processing from movies to 2D classes. Includes CTF estimation, quality filters, box size estimation, training a data-specific picking model, and three 2D classification jobs (25k, 50k, and 100k particles) using CryoSPARC.

Adapting to Tilted Samples

To process tilted experiments, use ”tilted” templates. These are modified workflows tailored to handle high drift and lower resolution commonly observed in tilted samples. Key adjustments include:

  • Motion Correction Filters: ...

Type: Scipion

Creators: None

Submitter: Daniel Marchan

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