metagenomix 2.4.0

metagenomix is a pipeline of pipelines to conduct metagenomic analyses on Slurm/Torque

metagenomix

WRITING IN PROGRESS...

Description

metagenomix is a pipeline creator, monitor and manager that takes care of writing the command-lines for any shotgun metagenomics software, either as bash scripts or Slurm/Torque jobs (incl. scratch space usage), following user-defined configurations for databases, co-assemblies, strain foci, as well as software- specific or computing resource parameters (incl. modules and condenvironments).

Any software? Well, if not already in the softwares list, someone will need to add it to metagenomix, following these instructions.

This also eases importing issues and notably run this on a High-Performance Computer (HPC), either Torque or Slurm scheduler, and it heavily relies on a you having installed and configured properly multiple conda environments (explanations and environment.yml files provided in Wiki). This tool wrapping other tools could be done using snakemake but this is meant to only create the scripts to run on your samples, not execute these scripts.

Installation

pip install --upgrade git+https://github.com/FranckLejzerowicz/metagenomix.git

*Note that python and pip should be python3

Depencency for jobs preparation

Xpbs must be installed as it allows automatic preparation of HPC scripts from the basic bash scripts written here. For Xpbs to work, it is necessary that the user provide edit the config.txt file of this tool (simply adding the email address for job completion as explained here).

Depencencies for jobs to run

You must install all the databases and softwares (lists below) that the pipeline will allow you to run. I recommend using conda environments for each tool and then specify the name of the environment for this tool in the run parameters configuration file. I am working on an installer of conda environments to alleviate this time-consuming step, but since some tools may require you to edit configurations for you system, this will not be fully integrated.

Databases

• PFAM: allows searching HMM profiles per keywords from the Pfam-A catalogue, (see here or here) which you need to download: Pfam-A files "Pfam-A.hmm" and "Pfam-A.hmm.dat.gz" here

• dbCAN: allows searching HMM profiles per CAZy subfamily.

• MAR: Allow querying the MarDB and MarRef databases for marine microbes.

• GTDB

Softwares

• Antismash Search genomes for secondary metabolite biosynthetic gene clusters(paper)
• Anvi'o (paper Integrated multi-omics at scale. paper)
• atropos Trimming. (paper)
• CheckM Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes. (paper)
• cutadapt Quality control. (paper)
• DeepVirFinder Identifying viruses from metagenomic data by (deep learning). (paper)
• DIAMOND Accelerated BLAST compatible local sequence aligner. (paper)
• dRep Rapid comparison and dereplication of genomes. (paper)
• FastQC A quality control analysis tool for high throughput sequencing data.
• FLASh Overlapping reads pairs merging. (paper)
• graphlan High-quality circular representations of taxonomic and phylogenetic trees.
• GRASP2 gene-centric homolog search tool (paper)
• GroopM Metagenomic binning suite. (paper)
• GTDB-tk Taxonomic classification of bacterial and archaeal genomes based on GTDB. (paper)
• HUMAnN 3 Abundance profiling of microbial taxa and metabolic pathways. (paper)
• I-TASSER Protein structure prediction and structure-based function annotation. (paper)
• Integron_Finder Find integrons in bacterial genomes. (paper)
• inStrain Stain-level analyses for co-occurring genome populations. (paper)
• IonCom Ligand-specific method for small ligand (including metal and acid radical ions) binding site prediction. (paper)
• Kneadata Quality control.
• Kraken2 (paper)
• MacSyFinder Detection of macromolecular systems in protein datasets using systems modelling and similarity search. (paper)
• mapDamage2 Tracking and quantifying damage patterns in ancient DNA sequences. (paper)
• metaclade2 Multi-source domain annotation. (paper)
• Metamarker De novo pipeline to discover novel metagenomic biomarkers. (paper)
• metaphlan Taxon abundance profiler based on clade-specific marker genes from ~17,000 reference genomes. (paper)
• MAC Merging assemblies by using adjacency algebraic model and classification. paper
• MetaWRAP Flexible pipeline for genome-resolved metagenomic data analysis. (paper)
• Metaxa2 Identification and taxonomic classification of SSU and LSU rRNA in metagenomes. (paper)
• MIDAS Strain-level genomic variation (paper)
• MOCAT2 Taxonomic and functional abundance profiling, reads assembler and gene prediction. (paper)
• MultiQC Quality control. (paper)
• panphlan Strain-level profiler for gene composition of individual strains. (paper)
• PhyloFlash Reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset. (paper)
• phylophlan (paper)
• PLASS Protein-Level ASSembler (paper)
• Prokka Rapid prokaryotic genome annotation (paper)
• Prodigal Gene Prediction (paper)
• QUAST Genome assembly evaluation tool. (paper)
• run_dbcan Search for CAZymes. (paper)
• seqtk Toolkit for processing sequences in FASTA/Q formats. (paper)
• SHOGUN Taxonomic and functional profiling. (paper)
• SignalP Predicts presence of signal peptides and location of their cleavage sites in proteins. (paper)
• Simka De novo metagenomes comparison using k-mer spectra and classical ecological distances. (paper)
• SPAdes Assembler. (paper)
• SqueezeMeta Complete pipeline for metagenomic analysis. (paper)
• strainphlan Strain-level population genomics tool. (paper)
• strainsifter Detection of a bacterial strain in one or more metagenome(s). (paper)
• StrainPro Strain-level profiling. (paper)
• TMHMM Prediction of transmembrane helices in proteins. (paper)
• vamb Variational autoencoder for metagenomic binning. (paper)
• VirStrain RNA virus strain-level identification for short reads. (paper)
• Woltka Taxonomic and functional profiling. preprint
• WIsH Predict prokaryotic hosts from metagenomic phage contigs (paper)
• YAMB Yet Another Metagenome Binner - semi-automatic pipeline for metagenomic contigs binning. (paper)
• Will keep growing - that's the point of this pipeline

Plasmid detection

• Deeplasmid Separates plasmids from chromosomal sequences (ML). (paper)
• PlasForest homology-based random forest classifier for plasmid detection in genomic datasets. paper

Will keep growing - that's the point of this pipeline

Input

IN CONSTRUCTION

Outputs

IN CONSTRUCTION