Workflows

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604 Workflows visible to you, out of a total of 648
repeatmasking/main

RepeatMasking Workflow

This workflow uses RepeatModeler and RepeatMasker for genome analysis.

  • RepeatModeler is a software package for identifying and modeling de novo families of transposable elements (TEs). At the heart of RepeatModeler are three de novo repeat search programs (RECON, RepeatScout and LtrHarvest/Ltr_retriever) which use complementary computational methods to identify repeat element boundaries and family relationships from sequence data.

  • RepeatMasker is a program that analyzes ...

Type: Galaxy

Creator: Romane Libouban

Submitter: WorkflowHub Bot

average-bigwig-between-replicates/main

We assume the identifiers of the input list are like: sample_name_replicateID. The identifiers of the output list will be: sample_name

Type: Galaxy

Creator: Lucille Delisle

Submitter: WorkflowHub Bot

sars-cov-2-pe-illumina-artic-variant-calling/COVID-19-PE-ARTIC-ILLUMINA

The workflow for Illumina-sequenced ARTIC data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming ARTIC primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by ARTIC primer-binding site mutations and tries to exclude reads derived from such tainted amplicons when calculating allele-frequencies of other variants.

Type: Galaxy

Creator: Wolfgang Maier

Submitter: WorkflowHub Bot

openms-metaprosip/main

Automated inference of stable isotope incorporation rates in proteins for functional metaproteomics

Type: Galaxy

Creator: Matthias Bernt

Submitter: WorkflowHub Bot

baredsc/baredSC-1d-logNorm

Run baredSC in 1 dimension in logNorm for 1 to N gaussians and combine models.

Type: Galaxy

Creator: Lucille Delisle

Submitter: WorkflowHub Bot

kmer-profiling-hifi-VGP1/main

VGP Workflow #1

This workflow produces a Meryl database and Genomescope outputs that will be used to determine parameters for following workflows, and assess the quality of genome assemblies. Specifically, it provides information about the genomic complexity, such as the genome size and levels of heterozygosity and repeat content, as well about the data quality.

Inputs

  • A collection of Hifi long reads in FASTQ format
  • k-mer length
  • Ploidy

Outputs

  • Meryl Database of kmer counts

...

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

kmer-profiling-hifi-trio-VGP2/main

Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

Assembly-decontamination-VGP9/main
No description specified

Type: Galaxy

Creator: Nadolina Brajuka

Submitter: WorkflowHub Bot

lcms-preprocessing/main

This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract, filter, align and fill gapand the possibility to annotate isotopes, adducts and fragments using the CAMERA R package (Kuhl, C 2012).

https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html

Type: Galaxy

Creator: workflow4metabolomics

Submitter: WorkflowHub Bot

gcms-metams/main

This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract and the metaMS R package (Wehrens, R 2014) for the field of untargeted metabolomics.

https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/gcms/tutorial.html

Type: Galaxy

Creator: workflow4metabolomics

Submitter: WorkflowHub Bot

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