This workflow perform the scaffolding of a genome assemble using HiC data with YAHS. Part of the VGP set of workflows.

This workflow generates Hi-C contact maps for genome assemblies in the Pretext format. It is compatible with one or 2 haplotypes. It includes tracks for PacBio read coverage, Gaps, and telomeres. The Pretext files can be open in PretextView for the manual curation of genome assemblies.

Genome Assembly with Hifi reads and Trio Data

Generate phased assembly based on PacBio Hifi Reads using parental Illumina data for phasing. Part of the VGP workflow suite, it needs to be run after the Trio k-mer Profiling workflow VGP2.

Inputs

1. Hifi long reads [fastq]
2. Concatenated Illumina reads : Paternal [fastq]
3. Concatenated Illumina reads : Maternal [fastq]
4. K-mer database [meryldb] generated by VGP2 workflow.
5. Paternal hapmer database [meryldb] generated by VGP2 workflow.

...

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)

Purge duplicates from one haplotype. Prerequisites: run after a k-mer profiling workflow (VGP 1 or 2) and a contiging workflow (VGP 3,4 or 5).

Contiging Solo:

Generate assembly based on PacBio Hifi Reads.

Inputs

1. Hifi long reads [fastq]
2. K-mer database [meryldb]
3. Genome profile summary generated by Genomescope [txt]
4. Homozygous Read Coverage. Optional, use if you think the estimation from Genomescope is inacurate.
5. Genomescope Model Parameters generated by Genomescope [tabular]
6. Database for busco lineage (recommended: latest)
7. Busco lineage (recommended: vertebrata)
8. Name of first assembly
9. Name of second ...

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

Microbiome - Variant calling and Consensus Building

Build a consensus sequence from FILTER PASS variants with intrasample allele-frequency above a configurable consensus threshold. Hard-mask regions with low coverage (but not consensus variants within them) and ambiguous sites.

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 ...

This workflows performs single end read mapping with bowtie2 followed by sensitive variant calling across a wide range of AFs with lofreq

This workflow runs the FEELnc tool to annotate long non-coding RNAs. Before annotating these long non-coding RNAs, StringTie will be used to assemble the RNA-seq alignments into potential trancriptions. The gffread tool provides a genome annotation file in GTF format.

Decontamination Workflow

Decontamination (foreign contaminants and mitochondrial sequences) of genome assembly after scaffolding step. Part of the VGP Suite.

Inputs

• Genome Assembly [fasta]
• Database for Kraken2. Database containing the possible contaminants.

Ouput

• List of contaminant scaffolds
• List of mitochondrial scaffolds
• Decontaminated assembly

This workflow allows for genome annotation using Maker and evaluates the quality of the annotation.

This workflow creates taxonomic summary tables for a specified taxonomic rank out of MAPseq's OTU tables output collection.

The MAPseq to Ampvis workflow processes MAPseq OTU tables and associated metadata for analysis in Ampvis2. This workflow involves reformatting MAPseq output datasets to produce structured output files suitable for Ampvis2.

MGnify's amplicon pipeline v5.0. Including the Quality control for single-end and paired-end reads, rRNA-prediction, and ITS sub-WFs.

Classification and visualization of ITS regions.

Quality control subworkflow for paired-end reads.

Quality control subworkflow for single-end reads.