Contiging Solo w/HiC:

Generate phased assembly based on PacBio Hifi Reads using HiC data from the same individual for phasing.

Inputs

1. Hifi long reads [fastq]
2. HiC forward reads (if multiple input files, concatenated in same order as reverse reads) [fastq]
3. HiC reverse reads (if multiple input files, concatenated in same order as forward reads) [fastq]
4. K-mer database [meryldb]
5. Genome profile summary generated by Genomescope [txt]
6. Name of first assembly
7. Name of second ...

Assembly with Hifi reads and Trio Data

Generate phased assembly based on PacBio Hifi Reads using parental Illumina data for phasing

Inputs

1. Hifi long reads [fastq]
2. Concatenated Illumina reads : Paternal [fastq]
3. Concatenated Illumina reads : Maternal [fastq]
4. K-mer database [meryldb]
5. Paternal hapmer database [meryldb]
6. Maternal hapmer database [meryldb]
7. Genome profile summary generated by Genomescope [txt]
8. Genome model parameters generated by Genomescope [tabular]

...

Microbiome - Variant calling and Consensus Building

Nanopore datasets analysis - Phylogenetic Identification - antibiotic resistance genes detection and contigs building

Microbiome - QC and Contamination Filtering

Pathogens of all samples report generation and visualization

Microbiome - Taxonomy Profiling

Generate Nx and Size plot for multiple assemblies

Inputs

Collection of fasta files. The name of each item in the collection will be used as label for the Nx and Size plots.

Outputs

1. Nx plot
2. Size plot

Short paired-end read analysis to provide quality analysis, read cleaning and taxonomy assignation

This workflow takes a collection of BAM (output of STAR) and a gtf. It extends the input gtf using de novo annotation.

Annotation of an assembled bacterial genomes to detect genes, potential plasmids, integrons and Insertion sequence (IS) elements.

Antimicrobial resistance gene detection from assembled bacterial genomes

Assembly of bacterial paired-end short read data with generation of quality metrics and reports

Purge Duplicate Contigs

Purge contigs marked as duplicates by purge_dups in a single haplotype(could be haplotypic duplication or overlap duplication) This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)

Inputs

1. Genomescope model parameters [txt] (Generated by the k-mer profiling workflow)
2. Hifi long reads - trimmed [fastq] (Generated by Cutadapt in the contigging workflow)
3. Assembly to purge (e.g. hap1) ...

Scaffolding using HiC data with YAHS.

Importing single-end multiplexed data (not demultiplexed yet)

Use DADA2 for sequence quality control. DADA2 is a pipeline for detecting and correcting (where possible) Illumina amplicon sequence data. As implemented in the q2-dada2 plugin, this quality control process will additionally filter any phiX reads (commonly present in marker gene Illumina sequence data) that are identified in the sequencing data, and will filter chimeric sequences.

Purge contigs marked as duplicates by purge_dups (could be haplotypic duplication or overlap duplication). This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)

Scaffolding with Bionano

Scaffolding using Bionano optical map data

Inputs

1. Bionano data [cmap]
2. Estimated genome size [txt]
3. Phased assembly generated by Hifiasm [gfa1]

Outputs

1. Scaffolds
2. Non-scaffolded contigs
3. QC: Assembly statistics
4. QC: Nx plot
5. QC: Size plot