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List of workflows (nextflow/snakemake) tested for Genotoul Cluster.

Pipeline Nextflow

panTEannot serially annotates transposable elements from multiple genomes using a common reference library. The annotation is a light version of TEannot from REPET package. These annotations can be used as input for the panREPET tool.

ICEscreen detects and annotates ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Firmicutes genomes.

scripts to remap markers as pairs of bait sequences or context sequences.

RNAseq and EMseq analyses for the rosepigs project on stomach mucosa samples

Implements in R the Rothamsted RothC package. Adds useful functions.

Harvest and index meta data from BrAPI endpoints for data access through the plant-faidare data lookup portal (https://github.com/elixir-europe/plant-faidare).

The aim of this project is to provide an R package for big integer (and big rational) computations. This is achieved via an C++ interface to the GNU MP ("GMP") library, and S3 classes "bigz", "bigq", etc.

Docker image with Intel Fortran Compiler (and some other dev tools).

Example GitBook site using GitLab Pages: https://pages.gitlab.io/gitbook