Alise Ponsero's repositories
HPC_ViralDetection
Parallel pipeline using Virsorter2 and DeepVirFinder to identify viral contigs from WGS assemblies
MAGs_annotate
Parallelized pipeline (SLURM scheduler) for MAGs functional annotation
Sequence_analysis_Workshop_2021
KEYS workshop: what can we learn from a single sequence?
Aggregated_Viral_Catalogue
User interface for the AVrC
canopy2_conda
canopy clustering of gene catalogues
CURE_interface
Interface for the CURE class - Data science heroes
dada2_16Sprocessing
Simple pipeline for 16S taxonomic analysis using dada2
HPC_assembly
HPC pipeline for parrallel assembly of WGS metagenomes (SLURM)
HPC_DiamondX
Pipeline for parrallel submission of BLASTX diamond jobs (SLURM scheduler)
HPC_dRep_MAGs
HPC pipeline to dereplicate MAGs using dRep
HPC_Kraken2_KrakenTools
Parrallel pipeline for Kraken2 and KrakenTools (SLURM)
HPC_KrakenFor16S
HPC pipeline for 16S taxonomic profiling using Kraken2
HPC_QC_humanReads
QC and human read removal parallel pipeline for HPC (SLURM)
Humann_annotation_HPC
Pipeline for the parrallel use of Humann (functional annotation of metagenomes) in HPC - Slurm scheduler
lichen_mock_metagenomes
Pipeline to generate mock lichen metagenomes. Parralelized for a HPC use
MAGs_HPCpipeline
Parralelized pipeline (SLURM scheduler) for the generation of MAGs
MAGs_ViralFinder
Pipeline for the detection and characterization of prophages sequences in genomes and MAGs
quadram-institute-bioscience.github.io
Core Bioinformatics public page
Resistome_ReadBased_Snakemake
Snakemake pipeline for Resistome and Mobilome annotation of unassembled metagenomes
Rvisualisations_tidytuesday
Learning R vizualisation and data wrangling through the awesome tidytuesday !
SRA_download
Script to download a list of runs from SRA. Pipeline for HPC with SLURM scheduler
Taxonomy_Functional_HPCpipeline
Parrallel pipeline for HPC (Slurm scheduler) for the QC, taxonomic annotation and functional profiling of WGS metagenomes
tidytuesday
Official repo for the #tidytuesday project
transition_plot_function
Visualization of between-time point cluster transitions
Tutorial_QC_TaxAnnotation
Simple Tutorial for performing QC and Taxonomic annotation on Whole Genome Shotgun on HPC system
ViCAT_dev
Virus community assembly tool for HPC with SLURM scheduler
Viral_confirmation_snakemake
Snakemake pipeline to confirm the viral origin of selected sequences
Web-page-perso
simple web for professional portfolio
Web-page-Val
professional portfolio for V. Ponsero