Workflows

The workflow takes a paired-reads collection (like illumina WGS or HiC), runs FastQC and SeqKit, trims with Fastp, and creates a MultiQC report. The main outputs are a paired collection of trimmed reads, a report with raw and trimmed reads stats, and a table with raw reads stats.

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 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.

The workflow takes a (trimmed) Long reads collection, runs Meryl to create a K-mer database, Genomescope2 to estimate genome properties and Smudgeplot to estimate ploidy (optional). 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 31 and 2, respectively.

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

The workflow takes trimmed HiC paired-end reads collection, and Pri/Alt assemblies to produce a scaffolded primary assembly (and alternate contigs) using YaHS. It also runs Pretext and all the QC analyses (gfastats, BUSCO, and Merqury).

The workflow takes a long reads collection (HiFi, or ONT also possible now), and max coverage depth (calculated from WF1) to run Hifiasm in solo mode. It produces a Pri/Alt assembly, Bandage plots, and runs all the QC analysis (gfastats, BUSCO, and Merqury).

The workflow requires the user to provide:

• ENSEMBL link address of the annotation GFF3 file
• ENSEMBL link address of the assembly FASTA file
• NCBI taxonomy ID
• BUSCO lineage
• OMArk database

Thw workflow will produce statistics of the annotation based on AGAT, BUSCO and OMArk.

Assembly Evaluation for ERGA-BGE Reports

One Assembly, Illumina WGS reads + HiC reads

The workflow requires the following:

• Species Taxonomy ID number
• NCBI Genome assembly accession code
• BUSCO Lineage
• WGS accurate reads accession code
• NCBI HiC reads accession code

The workflow will get the data and process it to generate genome profiling (genomescope, smudgeplot -optional-), assembly stats (gfastats), merqury stats (QV, completeness), BUSCO, snailplot, contamination blobplot, and ...

Assembly Evaluation for ERGA-BGE Reports

One Assembly, HiFi WGS reads + HiC reads

The workflow requires the following:

• Species Taxonomy ID number
• NCBI Genome assembly accession code
• BUSCO Lineage
• WGS accurate reads accession code
• NCBI HiC reads accession code

The workflow will get the data and process it to generate genome profiling (genomescope, smudgeplot -optional-), assembly stats (gfastats), merqury stats (QV, completeness), BUSCO, snailplot, contamination blobplot, and HiC ...