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 ...

This workflow provides a calculaiton 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) ...

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 ...

With this galaxy pipeline you can use Salmonella sp. next generation sequencing results to predict bacterial AMR phenotypes and compare the results against gold standard Salmonella sp. phenotypes obtained from food.

This pipeline is based on the work of the National Food Agency of Canada. Doi: 10.3389/fmicb.2020.00549

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 ...

skim2mt

skim2mt is a snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes 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

...