Performs Long Read assembly using PacBio data and Hifiasm. Part of VGP assembly pipeline. This workflow generate a phased assembly.

Performs scaffolding using HiC Data. Part of VGP assembly pipeline. The scaffolding can be performed on long read assembly contigs or on scaffolds (e.g.: Bionano scaffolds).

Performs scaffolding using Bionano Data. Part of VGP assembly pipeline.

Purge Phased assembly of duplications and overlaps. Include purge steps for Primary and Alternate assemblies.

Performs Long Read assembly using PacBio data and Hifiasm. Part of VGP assembly pipeline. This workflow generate a phased assembly.

Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.

eQTL-Catalogue/qtlmap

Portable eQTL analysis and statistical fine mapping workflow used by the eQTL Catalogue

Introduction

eQTL-Catalogue/qtlmap is a bioinformatics analysis pipeline used for QTL Analysis.

The workflow takes phenotype count matrix (normalized and quality controlled) and genotype data as input, and finds associations between them with the help of sample metadata and phenotype metadata files (See Input formats and preparation for required input ...

This workflow demonstrates the usage of EODIE, a toolkit to extract object based timeseries information from Earth Observation data.

EODIE is a toolkit to extract object based timeseries information from Earth Observation data.

The EODIE code can be found on Gitlab .

The goal of EODIE is to ease the extraction of time series information at object level. Today, vast amounts of Earth Observation data are available to the users via for example earth explorer ...

Summary

This notebook demonstrates how to recreate lineages published in the paper Live imaging of remyelination in the adult mouse corpus callosum and available at idr0113-bottes-opcclones.

The lineage is created from the metadata associated to the specified image.

To load the data from the Image Data Resource, we use:

• the Python API ...

ASPICov was developed to provide a rapid, reliable and complete analysis of NGS SARS-Cov2 samples to the biologist. This broad application tool allows to process samples from either capture or amplicon strategy and Illumina or Ion Torrent technology. To ensure FAIR data analysis, this Nextflow pipeline follows nf-core guidelines and use Singularity containers.

Availability and Implementation: https://gitlab.com/vtilloy/aspicov

Citation: Valentin Tilloy, Pierre Cuzin, Laura Leroi, Emilie Guérin, ...