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 raw ONT reads and trimmed Illumina WGS paired reads collections, and the estimated genome size and Max depth (both calculated from WF1) to run Flye and subsequently polish the assembly with HyPo. It produces collapsed assemblies (unpolished and polished) and runs all the QC analyses (gfastats, BUSCO, and Merqury).

The workflow takes trimmed HiC forward and reverse reads, and one assembly (e.g.: Hap1 or Pri or Collapsed) to produce a scaffolded assembly using YaHS. It also runs all the QC analyses (gfastats, BUSCO, and Merqury).

The workflow takes a trimmed Illumina WGS paired-end reads collection, Collapsed contigs, and the values for transition parameter and max coverage depth (calculated from WF1) to run Purge_Dups. It produces purged Collapsed contigs assemblies, and runs all the QC analysis (gfastats, BUSCO, and Merqury).

The workflow takes a trimmed Illumina paired-end 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 ddatabase 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 ONT reads collection, runs SeqKit and Nanoplot. The main outputs are a table and plots of raw reads stats.