Credits
Cecret is a nextflow workflow that strings together a variety of tools, and would not be possible without them.
- Cecret lake images copied from https://intermountainhealthcare.org/locations/live-well-centers/services/sports-performance-services.
- Png images for tools were generated by Cecret developers.
- aci - for depth estimation over amplicons
- artic network - for aligning and consensus creation of nanopore reads
- bcftools - for variant identification
- bwa - for aligning reads to the reference
- fastp - for cleaning reads ; optional, faster alternative to seqyclean
- fastqc - for QC metrics
- freyja - for multiple SARS-CoV-2 lineage classifications
- heatcluster - for visualization of SNP matrix
- igv-reports for variant visualization
- iqtree2 - for phylogenetic tree generation (optional, relatedness must be set to "true")
- ivar - calling variants and creating a consensus fasta; optional primer trimmer
- kraken2 - for read classification
- mafft - for multiple sequence alignment (optional, relatedness must be set to "true")
- minimap2 - an alternative to bwa
- multiqc - summary of results
- nextalign - for phylogenetic tree generation (optional, relatedness must be set to "true", and msa must be set to "nextalign")
- nextclade - for SARS-CoV-2 clade classification
- pango-collapse - for pangolin lineage tracing
- pangolin - for SARS-CoV-2 lineage classification
- phytreeviz - for visualization of newick file
- samtools - for QC metrics and sorting; optional primer trimmer; optional converting bam to fastq files; optional duplication marking
- seqyclean - for cleaning reads
- snp-dists - for relatedness determination (optional, relatedness must be set to "true")
- vadr - for annotating fastas like NCBI
Something like "fastq files underwent assembly and analysis via the Cecret workflow (https://github.com/UPHL-BioNGS/Cecret) version XXXX".
