https://orcid.org/0009-0003-9935-828X
Teams: Cimorgh IT solutions
Organizations: cimorgh IT
I am a bioinformatician working on microbial ecology and ecosystem functioning at the microbial dimension.
Dad, husband and PhD. Scientist, technologist and engineer. Bibliophile. Philomath. Passionate about science, medicine, research, computing and all things geeky!
Abstract (Expand)
Authors: Alex L Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, Varsha Kale, Simon C Potter, Lorna J Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyavskaya, Alla Lapidus, Robert D Finn
Date Published: 7th Nov 2019
Publication Type: Journal
Tests 
The aim of this workflow is to handle the routine part of shotgun metagenomics data processing. The workflow is using the tools Kraken2 and Bracken for taxonomy classification and the KrakenTools to evaluate diversity metrics. This workflow was tested on Galaxy Australia. A How-to guide for the workflow can be found at: https://github.com/vmurigneu/kraken_howto_ga_workflows/blob/main/pages/taxonomy_kraken2_wf_guide.md
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
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
Type: Nextflow
Creators: No author provided, Hadrien Gourlé, Daniel Straub, Sabrina Krakau
Submitter: WorkflowHub Bot
Type: Nextflow
Creators: Jasmin Frangenberg, Anan Ibrahim, James A. Fellows Yates
Submitter: WorkflowHub Bot
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Type: Nextflow
Creators: Alexander Peltzer, The nf-core/eager community, Stephen Clayton, James A Fellows-Yates
Submitter: WorkflowHub Bot
A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxa to identify (and remove) are Homo and Homo sapiens. Removal is optional.
The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for pipeline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.
Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...
Type: Galaxy
Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi
Submitter: Sarah Williams
The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for pipeline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.
Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...
Type: Galaxy
Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi
Submitter: Sarah Williams
The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for pipeline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.
Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...
Type: Galaxy
Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi
Submitter: Sarah Williams
The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for pipeline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.
Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...
Type: Galaxy
Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi
Submitter: Sarah Williams
The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for piepline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.
Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...
Type: Galaxy
Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi
Submitter: Sarah Williams
16S Microbial Analysis with mothur (short)
The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for piepline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.
Please also refer to the 16S tutorials available at Galaxy ...
Type: Galaxy
Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi
Submitter: Sarah Williams
The aim of this workflow is to handle the routine part of shotgun metagenomics data processing on Galaxy Australia.
The workflow is using the tools MetaPhlAn2 for taxonomy classification and HUMAnN2 for functional profiling of the metagenomes. The workflow is based on the Galaxy Training tutorial 'Analyses of metagenomics data - The global picture' (Saskia Hiltemann, Bérénice Batut) https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/general-tutorial/tutorial.html#shotgun-metagenomics-data. ...
Type: Galaxy
Creators: Valentine Murigneux, Mike Thang, Saskia Hiltemann, Bérénice Batut, The workflow is based on the Galaxy Training tutorial Analyses of metagenomics data. Thank you to the Galaxy Australia team, Igor Makunin and Mike Thang for help with the workflow
Submitter: Valentine Murigneux
About SnakeMAGs
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 ...
MGnify genomes catalogue 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 ...
Type: Nextflow
Creators: Ekaterina Sakharova, Tatiana Gurbich, Martin Beracochea
Submitter: Martin Beracochea
Assembly and quantification metatranscriptome using metagenome data.
Version: see VERSION
Introduction
MetaGT is a bioinformatics analysis pipeline used for improving and quantification metatranscriptome assembly using metagenome data. The pipeline supports Illumina sequencing data and complete metagenome and metatranscriptome assemblies. The pipeline involves the alignment of metatranscriprome assembly to the metagenome assembly with further extracting CDSs, which are covered by ...
MoMofy
Module for integrative Mobilome prediction
Bacteria can acquire genetic material through horizontal gene transfer, allowing them to rapidly adapt to changing environmental conditions. These mobile genetic elements can be classified into three main categories: plasmids, phages, and integrons. Autonomous elements are those capable of excising themselves from the chromosome, reintegrating elsewhere, and potentially modifying the host's physiology. Small integrative elements like insertion ...
The containerised pipeline for profiling shotgun metagenomic data is derived from the MGnify pipeline raw-reads analyses, a well-established resource used for analyzing microbiome data. Key components:
- Quality control and decontamination
- rRNA and ncRNA detection using Rfam database
- Taxonomic classification of SSU and LSU regions
- Abundance analysis with mOTUs
Workflow for the GTN training "Antibiotic resistance detection"
Workflow for Metagenomics from bins to metabolic models (GEMs)
Summary
- Prodigal gene prediction
- CarveMe genome scale metabolic model reconstruction
- MEMOTE for metabolic model testing
- SMETANA Species METabolic interaction ANAlysis
Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default
All tool CWL files and other workflows can be found here: Tools: https://gitlab.com/m-unlock/cwl Workflows: https://gitlab.com/m-unlock/cwl/workflows
**How ...
Workflow (hybrid) metagenomic assembly and binning
- Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
- FastQC (control)
- fastp (quality trimming)
- kraken2 (taxonomy)
- bbmap contamination filter
- Workflow Longread Quality:
- NanoPlot (control)
- filtlong (quality trimming)
- kraken2 (taxonomy)
- minimap2 contamination filter
- Kraken2 taxonomic classification of FASTQ reads
- SPAdes/Flye (Assembly)
- Pilon/Medaka/PyPolCA (Assembly polishing)
- QUAST (Assembly ...
Type: Common Workflow Language
Creators: Bart Nijsse, Jasper Koehorst, Changlin Ke
Submitter: Bart Nijsse
MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline ...
Type: Common Workflow Language
Creators: Ekaterina Sakharova, Varsha Kale, Martin Beracochea, Alex L Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, Varsha Kale, Simon C Potter, Lorna J Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyavskaya, Alla Lapidus, Robert D Finn
Submitter: Martin Beracochea
MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline ...
Type: Common Workflow Language
Creator: Alex L Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, Varsha Kale, Simon C Potter, Lorna J Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyavskaya, Alla Lapidus, Robert D Finn
Submitter: Martin Beracochea
MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline ...
Type: Common Workflow Language
Creator: Alex L Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, Varsha Kale, Simon C Potter, Lorna J Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyavskaya, Alla Lapidus, Robert D Finn
Submitter: Martin Beracochea
- Deprecated -
See our updated hybrid assembly workflow: https://workflowhub.eu/workflows/367
And other workflows: https://workflowhub.eu/projects/16#workflows
Workflow for sequencing with ONT Nanopore data, from basecalled reads to (meta)assembly and binning
- Workflow Nanopore Quality
- Kraken2 taxonomic classification of FASTQ reads
- Flye (de-novo assembly)
- Medaka (assembly polishing)
- metaQUAST (assembly quality reports)
When Illumina reads are provided:
- Workflow ...
Type: Common Workflow Language
Creators: Bart Nijsse, Jasper Koehorst, Germán Royval
Submitter: Jasper Koehorst
Shotgun Metagenomics Analysis
Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more
Description
The input for this analysis is paired end next generation sequencing data from metagenomic samples. The workflow is designed to be modular, so that individual modules can be run depending on the nature of the metagenomics project at hand. More modules will be added as we develop them - this repo is a work in progress!
These scripts have been written ...
Type: Shell Script
Creators: Cali Willet, Rosemarie Sadsad, Tracy Chew, Smitha Sukumar, Elena Martinez, Christina Adler, Henry Lydecker, Fang Wang
Submitter: Tracy Chew
Workflow for Metagenomics binning from assembly
Minimal inputs are: Identifier, assembly (fasta) and a associated sorted BAM file
Summary
- MetaBAT2 (binning)
- MaxBin2 (binning)
- SemiBin (binning)
- DAS Tool (bin merging)
- EukRep (eukaryotic classification)
- CheckM (bin completeness and contamination)
- BUSCO (bin completeness)
- GTDB-Tk (bin taxonomic classification)
Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default
**All tool CWL ...
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