[1.0.0] - 2020-06-01 Initial release of nf-core/viralrecon, created with the nf-core template. This pipeline is a re-implementation of the SARS_Cov2_consensus-nf and SARS_Cov2_assembly-nf pipelines initially developed by Sarai Varona and Sara Monzon from BU-ISCIII. Porting both of these pipelines to nf-core was an international collaboration between numerous contributors and developers, led by Harshil Patel from the The Bioinformatics & Biostatistics Group at The Francis Crick Institute, London. We appreciated the need to have a portable, reproducible and scalable pipeline for the analysis of COVID-19 sequencing samples and so the Avengers Assembled! Pipeline summary Download samples via SRA, ENA or GEO ids (ENA FTP, parallel-fastq-dump; if required) Merge re-sequenced FastQ files (cat; if required) Read QC (FastQC) Adapter trimming (fastp) Variant calling Read alignment (Bowtie 2) Sort and index alignments (SAMtools) Primer sequence removal (iVar; amplicon data only) Duplicate read marking (picard; removal optional) Alignment-level QC (picard, SAMtools) Choice of multiple variant calling and consensus sequence generation routes (VarScan 2, BCFTools, BEDTools || iVar variants and consensus || BCFTools, BEDTools) Variant annotation (SnpEff, SnpSift) Consensus assessment report (QUAST) De novo assembly Primer trimming (Cutadapt; amplicon data only) Removal of host reads (Kraken 2) Choice of multiple assembly tools (SPAdes || metaSPAdes || Unicycler || minia) Blast to reference genome (blastn) Contiguate assembly (ABACAS) Assembly report (PlasmidID) Assembly assessment report (QUAST) Call variants relative to reference (Minimap2, seqwish, vg, Bandage) Variant annotation (SnpEff, SnpSift) Present QC and visualisation for raw read, alignment, assembly and variant calling results (MultiQC)