A hecatomb is a great sacrifice or an extensive loss. Heactomb the software empowers an analyst to make data driven decisions to 'sacrifice' false-positive viral reads from metagenomes to enrich for true-positive viral reads. This process frequently results in a great loss of suspected viral sequences / contigs.

For information about installation, usage, tutorial etc please refer to the documentation: https://hecatomb.readthedocs.io/en/latest/

Quick start guide

Install Hecatomb from Bioconda ...

JAX NGS Operations Nextflow DSL2 Pipelines

This repository contains production bioinformatic analysis pipelines for a variety of bulk 'omics data analysis. Please see the Wiki documentation associated with this repository for all documentation and available analysis workflows.

Complete workflow for TANGO as reported in Lecomte et al (2024), "Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling", Metabolic Eng. 83:24-38 https://doi.org/10.1016/j.ymben.2024.02.014

1. Parameters for individual models are obtained by optimization
2. Individual dynamics and community dynamics are simulated
3. Figures for the manuscript are assembled from the results.

ProGFASTAGen

The ProGFASTAGen (Protein-Graph-FASTA-Generator or ProtGraph-FASTA-Generator) repository contains workflows to generate so-called precursor-specific-FASTAs (using the precursors from MGF-files) including feature-peptides, like VARIANTs or CONFLICTs if desired, or global-FASTAs (as described in ProtGraph). The single workflow scripts have been implemented with Nextflow-DSL-2 ...

The input to this workflow is a data matrix of gene expression that was collected from a pediatric patient tumor patient from the KidsFirst Common Fund program [1]. The RNA-seq samples are the columns of the matrix, and the rows are the raw expression gene count for all human coding genes (Table 1). This data matrix is fed into TargetRanger [2] to screen for targets which are highly expressed in the tumor but lowly expressed across most healthy human tissues based on gene expression data collected ...

The tool provides a calculation of the power spectrum of Stochastic Gravitational Wave Backgorund (SGWB) from a first-order cosmological phase transition based on the parameterisations of Roper Pol et al. (2023). The power spectrum includes two components: from the sound waves excited by collisions of bubbles of the new phase and from the turbulence that is induced by these collisions.

The cosmological epoch of the phase transition is described by the temperature, T_star and by the number(s) of ...

gene2phylo

gene2phylo is a snakemake pipeline for batch phylogenetic analysis of a given set of input genes.

Contents

• Setup
• Example data
• Input
• Output
• Running your own data
• Getting help
• Citations

Setup

The pipeline is written in Snakemake and uses conda to install the necessary tools.

It is strongly recommended to install conda using Mambaforge. See details here ...

skim2rrna

skim2rrna is a snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of ribosomal genes from low coverage genome skims. The pipeline was designed to work with sequence data from museum collections. However, it should also work with genome skims from recently collected samples.

Contents

• Setup
• Example data
• Input
• Output
• Filtering contaminants
• [Assembly and annotation ...

score-assemblies

A Snakemake-wrapper for evaluating de novo bacterial genome assemblies, e.g. from Oxford Nanopore (ONT) or Illumina sequencing.

The workflow includes the following programs:

• pomoxis assess_assembly and assess_homopolymers
• dnadiff from the mummer package
• NucDiff
• QUAST
• BUSCO

...

ont-assembly-snake

A Snakemake wrapper for easily creating de novo bacterial genome assemblies from Oxford Nanopore (ONT) sequencing data, and optionally Illumina data, using any combination of read filtering, assembly, long and short read polishing, and reference-based polishing.

Included programs