prepareChIPs

This is a simple snakemake workflow template for preparing single-end ChIP-Seq data. The steps implemented are:

1. Download raw fastq files from SRA
2. Trim and Filter raw fastq files using AdapterRemoval
3. Align to the supplied genome using bowtie2
4. Deduplicate Alignments using Picard MarkDuplicates
5. Call Macs2 Peaks using macs2

A pdf of the rulegraph is available here

Full details for each step are given below. Any additional ...

BatchConvert

A command line tool for converting image data into either of the standard file formats OME-TIFF or OME-Zarr.

The tool wraps the dedicated file converters bfconvert and bioformats2raw to convert into OME-TIFF or OME-Zarr, respectively. The workflow management system NextFlow is used to perform conversion in parallel for batches of images.

The tool also wraps s3 and Aspera clients (go-mc and aspera-cli, respectively). ...

A CWL-based pipeline for calling small germline variants, namely SNPs and small INDELs, by processing data from Whole-genome Sequencing (WGS) or Targeted Sequencing (e.g., Whole-exome sequencing; WES) experiments.

On the respective GitHub folder are available:

• The CWL wrappers and subworkflows for the workflow
• A pre-configured YAML template, based on validation analysis of publicly available HTS data

Briefly, the workflow performs the following steps:

1. Quality control of Illumina reads ...

A CWL-based pipeline for calling small germline variants, namely SNPs and small INDELs, by processing data from Whole-genome Sequencing (WGS) or Targeted Sequencing (e.g., Whole-exome sequencing; WES) experiments.

On the respective GitHub folder are available:

• The CWL wrappers and subworkflows for the workflow
• A pre-configured YAML template, based on validation analysis of publicly available HTS data

Briefly, the workflow performs the following steps:

1. Quality control of Illumina reads ...

A CWL-based pipeline for processing ChIP-Seq data (FASTQ format) and performing:

• Peak calling
• Consensus peak count table generation
• Detection of super-enhancer regions
• Differential binding analysis

On the respective GitHub folder are available:

• The CWL wrappers for the workflow
• A pre-configured YAML template, based on validation analysis of publicly available HTS data
• Tables of metadata (EZH2_metadata_CLL.csv and H3K27me3_metadata_CLL.csv), based on the same validation ...

A CWL-based pipeline for processing RNA-Seq data (FASTQ format) and performing differential gene/transcript expression analysis.

On the respective GitHub folder are available:

• The CWL wrappers for the workflow
• A pre-configured YAML template, based on validation analysis of publicly available HTS data
• A table of metadata (mrna_cll_subsets_phenotypes.csv), based on the same validation analysis, to serve as an input example for the design of comparisons during differential expression ...

SARS-CoV-2 variant prediction using Read It And Keep, fastp, bbmap and iVar

The project allowed us to manage and build structured code scripts on the Jupyter Notebook, a simple web application which is user-friendly, flexible to use in the research community. The script is developed to address the specific needs of research between different platforms of dataset. These stakeholders have developed their own platforms for the annotation and standardisation of both data and metadata produced within their respective field. -The INFRAFRONTIER - European Mutant Mouse Archive ...