Workflows

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).

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 ...