COVID-19: variation analysis on ARTIC PE data

The workflow for Illumina-sequenced ampliconic data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming amplicon primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by primer-binding site mutations and, if possible, excludes reads derived from such ...

VGP Workflow #1

This workflow produces a Meryl database and Genomescope outputs that will be used to determine parameters for following workflows, and assess the quality of genome assemblies. Specifically, it provides information about the genomic complexity, such as the genome size and levels of heterozygosity and repeat content, as well about the data quality.

Inputs

• Collection of Hifi long reads in FASTQ format

Outputs

• Meryl Database of kmer counts
• GenomeScope
• Linear plot

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VGP Workflow #1

This workflow collects the metrics on the properties of the genome under consideration by analyzing the k-mer frequencies. It provides information about the genomic complexity, such as the genome size and levels of heterozygosity and repeat content, as well about the data quality. It uses reads from two parental genomes to partition long reads from the offspring into haplotype-specific k-mer databases.

Inputs

• Collection of Hifi long reads in FASTQ format
• Paternal short-read ...

Generic variation analysis on WGS PE data

This workflows performs paired end read mapping with bwa-mem followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff. The reference genome can be provided as a GenBank file.

COVID-19: variation analysis reporting

This workflow takes VCF datasets of variants produced by any of the variant calling workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates tabular reports of variants by samples and by variant, along with an overview plot of variants and their allele-frequencies across all samples.