SARS-Cov2_analysis_pipeline

Introduction

This repo will contain all the information we can collect about the bioinformatics analysis of SARS-Cov2. We will try to include:

1. General information about the virus: genomics, epidemiology, molecular mechanisms,etc
2. Wetlab protocols: we are no wetlab experts, here we collect another groups/bibliography approximations that are currently being used. Knowing the protocols is imperative for develop comprenhensive pipelines addecuated to the data.
3. Data resources: summary of resources for covid19 (raw data, genomes, etc) and sofware/pipelines/initiatives already going on so we can all share our knowledge.
4. Analysis pipelines: different analysis aproximations depending on the data: experiment (metagenomics, sispa, amplicons) and sequencing platform (Illumina, pacbio, nanopore).

Tasks to be done

1. Collect information about the virus.
2. Collect information about initiatives and or already on going pipelines, we don't want to reinvent the wheel, and even so we want to share and merge our expertise.
3. Collect and think about new aproximations for the analysis: phylogenomics, phylodinamics, protein modelling, etc.
4. Launch our pipelines in all available data.
5. Create new pipelines using nextflow framework, bioconda and/or containers (singularity and docker)