Scaffolding using HiC data with YAHS.

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]

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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)

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.

Classification and visualization of SSU, LSU sequences.

This workflow creates taxonomic summary tables out of the amplicon pipeline results.