The workflow takes ONT reads collection, runs SeqKit and Nanoplot. The main outputs are a table and plots of raw reads stats.

The workflow takes a trimmed HiFi reads collection, Hap1/Hap2 contigs, and the values for transition parameter and max coverage depth (calculated from WF1) to run Purge_Dups. It produces purged Hap1 and Hap2 contigs assemblies, and runs all the QC analysis (gfastats, BUSCO, and Merqury).

ANNOTATO - Annotation workflow To Annotate Them Oll

• ANNOTATO - Annotation workflow To Annotate Them Oll
• Overview of the workflow
• Input data
• Pipeline steps
• Output data
• Prerequisites
• Installation
• Running ANNOTATO
• Before running the pipeline (IMPORTANT) ...

The workflow takes trimmed HiC forward and reverse reads, and Hap1/Hap2 assemblies to produce Hap1 and Hap2 scaffolded assemblies using YaHS. It also runs all the QC analyses (gfastats, BUSCO, Merqury and Pretext).

The workflow takes a trimmed HiFi reads collection, Forward/Reverse HiC reads, and the max coverage depth (calculated from WF1) to run Hifiasm in HiC phasing mode. It produces both Pri/Alt and Hap1/Hap2 assemblies, and runs all the QC analysis (gfastats, BUSCO, and Merqury). The default Hifiasm purge level is Light (l1).

The workflow takes a trimmed HiFi reads collection, runs Meryl to create a K-mer database, Genomescope2 to estimate genome properties and Smudgeplot to estimate ploidy. The main results are K-mer database and genome profiling plots, tables, and values useful for downstream analysis. Default K-mer length and ploidy for Genomescope are 21 and 2, respectively.

The workflow takes a HiFi reads collection, runs FastQC and SeqKit, filters with Cutadapt, and creates a MultiQC report. The main outputs are a collection of filtred reads, a report with raw and filtered reads stats, and a table with raw reads stats.

ERGA Protein-coding gene annotation workflow.

Adapted from the work of Sagane Joye:

https://github.com/sdind/genome_annotation_workflow

Prerequisites

The following programs are required to run the workflow and the listed version were tested. It should be noted that older versions of snakemake are not compatible with newer versions of singularity as is noted here: https://github.com/nextflow-io/nextflow/issues/1659.

conda v 23.7.3 ...