nf-core/viralrecon: nf-core/viralrecon v1.0.0 - Mercury Bat

[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

1. Download samples via SRA, ENA or GEO ids (ENA FTP, parallel-fastq-dump; if required)
2. Merge re-sequenced FastQ files (cat; if required)
3. Read QC (FastQC)
4. Adapter trimming (fastp)
5. Variant calling
   1. Read alignment (Bowtie 2)
   2. Sort and index alignments (SAMtools)
   3. Primer sequence removal (iVar; amplicon data only)
   4. Duplicate read marking (picard; removal optional)
   5. Alignment-level QC (picard, SAMtools)
   6. 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)
6. De novo assembly
   1. Primer trimming (Cutadapt; amplicon data only)
   2. Removal of host reads (Kraken 2)
   3. 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)
7. Present QC and visualisation for raw read, alignment, assembly and variant calling results (MultiQC)