Workflows
What is a Workflow?Filters
PARROT-FJD
Pipeline of Analysis and Research of Rare diseases Optimized in Tblab - Fundación Jiménez Díaz. This is a germline variant calling pipeline implemented in Nextflow which performs mapping, SNV/INDEL calling and annotation, and CNV calling and annotation for targeted sequencing (gene panels and WES) and whole genome sequencing.
How to run this pipeline
The different tasks previously mention are divided into different workflows which are specified usig the --analysis
flag followed
...
Introduction
nf-CBRA-snvs (nf-core - CIBERER Bioinformatics for Rare diseases Analysis - Small Nucleotide Variant) is a workflow optimized for the analysis of rare diseases, designed to detect SNVs and INDELs in targeted sequencing data (CES/WES) as well as whole genome sequencing (WGS).
This pipeline is developed using Nextflow, a workflow management system that enables an easy execution across various computing environments. It uses Docker or Singularity containers, simplifying setup and ...
NanoFreeLunch
Detecting DNA modifications quantitatively from Nanopore data without using raw signals.
Installation
- Install Julia from https://julialang.org/. Do Not use Julia in containers like docker or singularity.
- Enter the folder of NanoFreeLunch and type
julia setup.jl
. - The executable can be found in build/bin/, add the folder to PATH or add softlink of the executable to the folder in your PATH.
Warning: you might experience slow package downloading or get error like ...
[!NOTE] All data files in the
src/ethos/tokenize/maps
directory are under the CC0 public domain waiver.
ETHOS - EHR foundation model
This repository implements Adaptive Risk Estimation System (ARES) for Hospital Mortality, ICU Admission, Prolonged Length of Stay, and Composite (HM+IU+PLoS). In addition, it contains all the experiments conducted in our paper (preprint). It builds on our previous work on EHR foundation models by completely reimplementing ...
Classification and visualization of ITS regions.
Associated Tutorial
This workflows is part of the tutorial MGnify v5.0 Amplicon Pipeline, available in the GTN
Features
- Includes a Galaxy Workflow Report
- Uses ...
The MAPseq to Ampvis workflow processes MAPseq OTU tables and associated metadata for analysis in Ampvis2. This workflow involves reformatting MAPseq output datasets to produce structured output files suitable for Ampvis2.
Associated Tutorial
This workflows is part of the tutorial MGnify v5.0 Amplicon Pipeline, available in the GTN
Features
...
Quality control subworkflow for paired-end reads.
Associated Tutorial
This workflows is part of the tutorial MGnify v5.0 Amplicon Pipeline, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): ...
MGnify's amplicon pipeline v5.0. Including the Quality control for single-end and paired-end reads, rRNA-prediction, and ITS sub-WFs.
Associated Tutorial
This workflows is part of the tutorial MGnify v5.0 Amplicon Pipeline, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Unsupervised Classification of Bone marrow cells
Associated Tutorial
This workflows is part of the tutorial Unsupervised Analysis of Bone Marrow Cells with Flexynesis, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a ...
This workflow creates taxonomic summary tables out of the amplicon pipeline results.
Associated Tutorial
This workflows is part of the tutorial MGnify v5.0 Amplicon Pipeline, available in the GTN
Features
- Includes a Galaxy Workflow Report
- Uses ...