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Theoretical fragment substructure generation and in silico mass spectral library high-resolution upcycling workflow
Work-in-progress

Galaxy Workflow Documentation: MS Finder Pipeline

This document outlines a MSFinder Galaxy workflow designed for peak annotation. The workflow consists of several steps aimed at preprocessing MS data, filtering, enhancing, and running MSFinder.

Step 1: Data Collection and Preprocessing

Collect if the inchi and smiles are missing from the dataset, and subsequently filter out the spectra which are missing inchi and smiles.

1.1 MSMetaEnhancer: Collect InChi, Isomeric_smiles, and Nominal_mass

...

Type: Galaxy

Creators: Zargham Ahmad, Helge Hecht, Elliott J. Price, Research Infrastructure RECETOX RI (No LM2018121) financed by the Ministry of Education, Youth and Sports, and Operational Programme Research, Development and Innovation - project CETOCOEN EXCELLENCE (No CZ.02.1.01/0.0/0.0/17_043/0009632).

Submitters: Helge Hecht, Zargham Ahmad

DOI: 10.48546/workflowhub.workflow.888.2

End-to-end spectra predictions: multi atoms dataset
Stable

Galaxy Workflow Documentation: In-Silico Mass Spectra Prediction Using Semi-Empirical Quantum Chemistry

Overview

This workflow predicts in-silico mass spectra using a semi-empirical quantum chemistry method. It involves generating and optimizing molecular conformers and simulating their mass spectra with computational chemistry tools. The workflow receives an SDF file as input and outputs the mass spectrum in MSP file format.

Type: Galaxy

Creators: Zargham Ahmad, Helge Hecht, Wudmir Rojas, RECETOX SpecDat

Submitter: Wudmir Rojas

DOI: 10.48546/workflowhub.workflow.897.1

nf-core/viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples

Type: Nextflow

Creators: Sarai Varona and Sara Monzon, Patel H, Varona S and Monzon S

Submitter: WorkflowHub Bot

nf-core/viralintegration

Integration of viral sequences in genomic data

Type: Nextflow

Creators: Alyssa Briggs, Edmund Miller

Submitter: WorkflowHub Bot

nf-core/taxprofiler

Taxonomic classification and profiling of shotgun metagenomic data

Type: Nextflow

Creators: James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, Lauri Mesilaakso, Thomas A. Christensen II, Jianhong Ou, Mahwash Jamy, Maxime Borry, Rafal Stepien, Tanja Normark

Submitter: WorkflowHub Bot

nf-core/spatialtranscriptomics

Spatial Transcriptomics

Type: Nextflow

Creators: Sergii Domanskyi, Jeffrey Chuang, Anuj Srivastava

Submitter: WorkflowHub Bot

nf-core/smrnaseq

Small RNA-Seq Best Practice Analysis Pipeline.

Type: Nextflow

Creators: Phil Ewels <phil.ewels@scilifelab.se>, P. Ewels <phil.ewels@scilifelab.se>, P. Ewels, Chuan Wang <chuan.wang@scilifelab.se>, C. Wang <chuan.wang@scilifelab.se>, C. Wang, Rickard Hammarén <rickard.hammaren@scilifelab.se>, R. Hammarén <rickard.hammaren@scilifelab.se>, R. Hammarén, Lorena Pantano <lorena.pantano@gmail.com>, L. Pantano <lorena.pantano@gmail.com>, L. Pantano

Submitter: WorkflowHub Bot

nf-core/slamseq

SLAMseq analysis using Slamdunk with various T>C conversion quantifications and QC

Type: Nextflow

Creator: Tobias Neumann

Submitter: WorkflowHub Bot

nf-core/scrnaseq

Pipeline for processing 10x Genomics single cell rnaseq data

Type: Nextflow

Creators: Peter J Bailey, Bailey PJ, Alexander Peltzer, Botvinnik O, Olga Botvinnik, Marques de Almeida F, Peltzer A, Sturm G

Submitter: WorkflowHub Bot

nf-core/sarek

An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing

Type: Nextflow

Creators: Maxime Garcia, Szilveszter Juhos

Submitter: WorkflowHub Bot

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