Teams: Not specified
Organizations: Not specifiedhttps://orcid.org/0000-0003-0429-2365
Biomedical Engineer working on preclinical image dataset repository and cross researching RIs
Teams: Not specified
Organizations: Not specifiedhttps://orcid.org/0000-0001-6440-6980
I am a Ph.D. student in Gong lab. I am interested in cancer genomics, including the mining of genetic risk determinants in cancer, functional prediction of genetic variants, tumor-associated molecular epidemiology, large-scale data integration, analysis, and mining, as well as the construction of bioinformatical data platforms.
Organizations: National Laboratory of Scientific Computinghttps://orcid.org/0000-0002-2151-7418
I am a bioinformatician and phylogenetics. I really love working on problems at the intersection of high-performance computing and scientific workflows applied to omics
Teams: Not specified
Organizations: Not specifiedhttps://orcid.org/0000-0002-1399-293X
Dad, husband and PhD. Scientist, technologist and engineer. Bibliophile. Philomath. Passionate about science, medicine, research, computing and all things geeky!
Organizations: Pondicherry Universityhttps://orcid.org/0000-0003-4854-8238
Ph.D. Student at Department of Bioinformatics, Pondicherry University
Teams: MAB - ATGC
Organizations: Centre National de la Recherche Scientifique (CNRS)https://orcid.org/0000-0003-1590-8313
Teams: GalaxyProject SARS-CoV-2, nf-core viralrecon, EOSC-Life - Demonstrator 7: Rare Diseases, iPC: individualizedPaediatricCure, EJPRD WP13 case-studies workflows, TransBioNet, OpenEBench, ELIXIR Proteomicshttps://orcid.org/0000-0003-4929-1219
Computer Engineer in Barcelona Supercomputing Center (BSC)
Organizations: SIB - Swiss Institute of Bioinformaticshttps://orcid.org/0000-0002-7561-0810
Medical doctor and bioinformatician
Developer from the Swiss Institute of Bioinformatics (SIB) Working at the Computational Biology Group (CBG) of ETH Zurich.
Diplom in Medicine. MSc in Bioinformatics and Proteomics.
I am also a ski teacher as a hobby.
This workflow represents the Default ML Pipeline for AutoML feature from MLme. Machine Learning Made Easy (MLme) is a novel tool that simplifies machine learning (ML) for researchers. By integrating four essential functionalities, namely data exploration, AutoML, CustomML, and visualization, MLme fulfills the diverse requirements of researchers while eliminating the need for extensive coding efforts. MLme serves as a valuable resource that empowers researchers of all technical levels to leverage ...
CLAWS (CNAG's Long-read Assembly Workflow in Snakemake)
Snakemake Pipeline used for de novo genome assembly @CNAG. It has been developed for Snakemake v6.0.5.
It accepts Oxford Nanopore Technologies (ONT) reads, PacBio HFi reads, illumina paired-end data, illumina 10X data and Hi-C reads. It does the preprocessing of the reads, assembly, polishing, purge_dups, scaffodling and different evaluation steps. By default it will preprocess the reads, run Flye + Hypo + purge_dups + yahs and evaluate ...
SnakeMAGs is a workflow to reconstruct prokaryotic genomes from metagenomes. The main purpose of SnakeMAGs is to process Illumina data from raw reads to metagenome-assembled genomes (MAGs). SnakeMAGs is efficient, easy to handle and flexible to different projects. The workflow is CeCILL licensed, implemented in Snakemake (run on multiple cores) and available ...
GERONIMO is a bioinformatics pipeline designed to conduct high-throughput homology searches of structural genes using covariance models. These models are based on the alignment of sequences and the consensus of secondary structures. The pipeline is built using Snakemake, a workflow management tool that allows for the reproducible execution of analyses on various computational platforms.
The idea for developing GERONIMO emerged from a comprehensive search for [telomerase ...
This is a simple
snakemake workflow template for preparing single-end ChIP-Seq data.
The steps implemented are:
- Download raw fastq files from SRA
- Trim and Filter raw fastq files using
- Align to the supplied genome using
- Deduplicate Alignments using
- Call Macs2 Peaks using
A pdf of the rulegraph is available here
Full details for each step are given below. Any additional ...
SINGLE-END workflow. Align reads on fasta reference/assembly using bwa mem, get a consensus, variants, mutation explanations.
- For "bcftools call" consensus step, the --ploidy file is in "Données partagées" (Shared Data) and must be imported in your history to use the worflow by providing this file (tells bcftools to consider haploid variant calling).
- SELECT the mot ADAPTED VADR MODEL for annotation (see vadr parameters).
Submitter: Fabrice Touzain
This repository hosts Metabolome Annotation Workflow (MAW). The workflow takes MS2 .mzML format data files as an input in R. It performs spectral database dereplication using R Package Spectra and compound database dereplication using SIRIUS OR MetFrag . Final candidate selection is done in Python using RDKit and PubChemPy.
MGnify genomes analysis pipeline
MGnify A pipeline to perform taxonomic and functional annotation and to generate a catalogue from a set of isolate and/or metagenome-assembled genomes (MAGs) using the workflow described in the following publication:
Gurbich TA, Almeida A, Beracochea M, Burdett T, Burgin J, Cochrane G, Raj S, Richardson L, Rogers AB, Sakharova E, Salazar GA and Finn RD. (2023) [MGnify Genomes: A Resource for Biome-specific Microbial Genome ...
Submitter: Martin Beracochea
:wrench: This pipeline is currently under development :wrench:
- User guide
- Infrastructure usage and recommendations
- Workflow summaries
- Component tools
- Additional notes
Collection of de-novo genome assembly workflows written for implementation in Galaxy
Input data should be PacBio HiFi reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads
Executing all workflows will output two, scaffolded, haplotype assemblies