Workflows

To perform Qualification, Nitrate Calibration, Validation of One Argo float or One Glider by using Neural Network and Climatology. Copy past before running and change calibration parametrization if necessary

Associated Tutorial

This workflows is part of the tutorial Nitrate DMQC for autonomous platforms such as Argo floats, available in the GTN ...

Generate mitochondrial assembly based on PacBio HiFi reads. Part of the VGP suite, it can be run at any time independently of the other workflows. This workflow uses MitoHiFi and a mitochondrial reference to assemble the mitochondrial genome from PacBio reads. You do not need to provide the reference yourself, only the Latin name of the species.

This workflow performs quality and contamination control analysis on assembled contigs to assess bacterial genome quality and taxonomic assignment

Short paired-end read analysis to provide quality analysis, read cleaning and taxonomy assignation directly from raw reads

This workflow processes the CMO fastqs with CITE-seq-Count and include the translation step required for cellPlex processing. In parallel it processes the Gene Expresion fastqs with STARsolo, filter cells with DropletUtils and reformat all outputs to be easily used by the function 'Read10X' from Seurat.

Complete ChIP-seq analysis for single-end sequencing data. Processes raw FASTQ files through adapter removal (cutadapt), alignment to reference genome (Bowtie2), and quality filtering (MAPQ >= 30). Peak calling with MACS2 uses either a fixed extension parameter or built-in model to identify protein-DNA binding sites. Generates alignment files, peak calls, and quality metrics for downstream analysis.

Complete ChIP-seq analysis for paired-end sequencing data. Processes raw FASTQ files through adapter removal (cutadapt), alignment to reference genome (Bowtie2), and stringent quality filtering (MAPQ >= 30, concordant pairs only). Peak calling with MACS2 optimized for paired-end reads identifies protein-DNA binding sites. Generates alignment files, peak calls, and quality metrics for downstream analysis.

Find and annotate variants in ampliconic SARS-CoV-2 Illumina sequencing data and classify samples with pangolin and nextclade

COVID-19: variation analysis on WGS PE data

This workflows performs paired end read mapping with bwa-mem followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff 4.5covid19.

Variant calling and consensus sequence generation for batches of Illumina PE sequenced viruses with uncomplicated and stable genome structure (like e.g. Morbilliviruses).