Tutorial and specification for packaging IEEE 2791-2020 (BioCompute Objects/BCOs) as RO-Crate Research Objects.

BioCompute Object (BCO) is a standard (IEEE 2791-2020) for describing computational workflows for regularory submission, e.g. a genomics workflow as part of personalized medicine.

RO-Crate is a community-based specification for research data packaging of Research Objects with rich metadata, based on open standards and vocabularies like JSON-LD and schema.org.

BCO RO-Crate is the combination ...

MGnify genomes analysis 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 ...

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). Therefore, input and output locations can be specified as local ...

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

mvgwas-nf

A pipeline for multi-trait genome-wide association studies (GWAS) using MANTA.

The pipeline performs the following analysis steps:

• Split genotype file
• Preprocess phenotype and covariate ...

sqtlseeker2-nf

A pipeline for splicing quantitative trait loci (sQTL) mapping.

The pipeline performs the following analysis steps:

• Index the genotype file
• Preprocess the transcript expression data
• Test for association between ...

GermlineStructuralV-nf

:wrench: This pipeline is currently under development :wrench:

• Description
• Diagram
• User guide
• Infrastructure usage and recommendations
• Benchmarking
• Workflow summaries
• Metadata
• Component tools
• Additional notes
• Help/FAQ/Troubleshooting

...

CoVigator pipeline: variant detection pipeline for Sars-CoV-2

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IndexReferenceFasta-nf

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• Description
• Diagram
• User guide
• Benchmarking
• Workflow summaries
• Metadata
• Component tools
• Required (minimum) inputs/parameters
• Additional notes
• Help/FAQ/Troubleshooting
• Acknowledgements/citations/credits ...

nf-core/circrna

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

Introduction

nf-core/circrna is a best-practice analysis pipeline for the quantification, miRNA target prediction and differential expression analysis of circular RNAs in paired-end RNA sequencing data.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes ...

SAMBA is a FAIR scalable workflow integrating, into a unique tool, state-of-the-art bioinformatics and statistical methods to conduct reproducible eDNA analyses using Nextflow. SAMBA starts processing by verifying integrity of raw reads and metadata. Then all bioinformatics processing is done using commonly used procedure (QIIME 2 and DADA2) but adds new steps relying on dbOTU3 and microDecon to build high quality ASV count tables. Extended statistical analyses are also performed. Finally, SAMBA ...

microPIPE was developed to automate high-quality complete bacterial genome assembly using Oxford Nanopore Sequencing in combination with Illumina sequencing.

To build microPIPE we evaluated the performance of several tools at each step of bacterial genome assembly, including basecalling, assembly, and polishing. Results at each step were validated using the high-quality ST131 Escherichia coli strain EC958 (GenBank: HG941718.1). After appraisal of each step, we selected the best combination of ...

ORSON combine state-of-the-art tools for annotation processes within a Nextflow pipeline: sequence similarity search (PLAST, BLAST or Diamond), functional annotation retrieval (BeeDeeM) and functional prediction (InterProScan). When required, BUSCO completness evaluation and eggNOG Orthogroup annotation can be activated. While ORSON results can be analyzed through the command-line, it also offers the possibility to be compatible with BlastViewer or Blast2GO graphical tools.

A porting of the Trinity RNA assembly pipeline, https://trinityrnaseq.github.io, that uses Nextflow to handle the underlying sub-tasks. This enables additional capabilities to better use HPC resources, such as packing of tasks to fill up nodes and use of node-local disks to improve I/O. By design, the pipeline separates the workflow logic (main file) and the cluster-specific configuration (config files), improving portability.

Based on a pipeline by Sydney Informatics Hub: ...

Rare disease researchers workflow is that they submit their raw data (fastq), run the mapping and variant calling RD-Connect pipeline and obtain unannotated gvcf files to further submit to the RD-Connect GPAP or analyse on their own.

This demonstrator focuses on the variant calling pipeline. The raw genomic data is processed using the RD-Connect pipeline (Laurie et al., 2016) running on the standards (GA4GH) compliant, interoperable container ...

A pipeline for mapping, calling, and annotation of SARS-CoV2 variants.

A workflow for mapping and consensus generation of SARS-CoV2 whole genome amplicon nanopore data implemented in the Nextflow framework. Reads are mapped to a reference genome using Minimap2 after trimming the amplicon primers with a fixed length at both ends of the amplicons using Cutadapt. The consensus is called using Pysam based on a majority read support threshold per position of the Minimap2 alignment and positions with less than 30x coverage are masked using ‘N’.

metaboigniter is bioinformatics pipeline for pre-processing of mass spectrometry-based metabolomics data. It can be used to perform quantification and identification based on MS1 and MS2 data. The backbone of pipeline is based on XCMS, OpenMS, CAMERA, MSnbase, MetFrag, CSIFingerID, CFM-ID, and several other customized tools to noise filtering, quantification and identification both for library and in-silico identification. Please go on to this page to learn how to use the workflow

The pipeline ...

RNA sequencing analysis pipeline using STAR, HISAT2 and Salmon with gene counts and quality control.

TronFlow is an open source collection of computational workflows originally conceived for tumor-normal somatic variant calling over whole exome data and the manipulation of BAM and VCF files with the aim of having comparable and analysis-ready data. Over time, we have extended it to germline variant calling, copy numbers and other related technologies and analyses.

Its modular architecture covers different analytical and methodological use cases that allow analysing FASTQ files into analysis-ready ...