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vipr3

Summary

ViPR assembles your viral NGS reads and analyses low frequency variants (quasispecies) in your data. ViPR3 is losely based on its predecessors: the original ViPR and ViPR2.

In a first step reads are quality trimmed and adapters removed with Skewer. Reads are then assembled in two different ways:

  • With Spades after digital normalization with bbnorm (part of BBTools)
  • With Tadpole (part of BBTools)

Resulting contigs are QCed (visualization only) with Mummer and then joined and gap-filled (if needed) with the user-provided reference. Trimmed reads will then be mapped against the two assemblies and also against the user-provided reference with BWA-MEM. Finally variants are called with LoFreq. A plot showing coverage and SNP allele frequency is produced for all three mappings.

On assembly quality

This pipeline runs two assemblers, because neither one is clearly the best. One way to judge the quality is to look at the coverage and SNP plots created in the mapping and variant calling steps (see below for file names). Higher coverage and fewer SNPs (especially those with frequencies >50%) means a better assembly.

Output

  • Reads directory: {sample}/reads/
  • Cleaned, joined reads used for mapping: {sample}/reads/R[12].fastq.gz
  • Assembly directory: {sample}/assembly/{method}
  • Mapping directory: {sample}/mapping/{method}
  • Contig visualization: {sample}/assembly/{method}/scaffolds.fasta_QC/nucmer.coords.png
  • Gap filled assembly: {sample}/assembly/{method}/scaffolds.fasta
  • Alignment: {sample}/mapping/{method}/{sample}.bwamem.lofreq.bam
  • Coverage: {sample}/mapping/{method}/{sample}.bwamem.lofreq.cov.gz
  • Variants: {sample}/mapping/{method}/{sample}.bwamem.lofreq.vcf.gz
  • Visualization of coverage and SNP allele frequency: {sample}/mapping/{method}/{sample}.bwamem.lofreq.plot.png

method is either tadpole or spades (and also input-ref for mapping). The mapping folders contain the corresponding reference as ref.fa symlink.

References