Workflows

Take an anndata file, and perform basic QC with scanpy. Produces a filtered AnnData object.

From the R1 and R2 fastq files of a single samples, make a scRNAseq counts matrix, and perform basic QC with scanpy. Then, do further processing by making a UMAP and clustering. Produces a processed AnnData

Take a scRNAseq counts matrix from a single sample, and perform basic QC with scanpy. Then, do further processing by making a UMAP and clustering. Produces a processed AnnData object.

From the R1 and R2 fastq files of a single samples, make a scRNAseq counts matrix, and perform basic QC with scanpy. Then, do further processing by making a UMAP and clustering. Produces a processed AnnData

Takes fastqs and reference data, to produce a single cell counts matrix into and save in annData format - adding a column called sample with the sample name.

MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data

microPIPE was developed to automate high-quality complete bacterial genome assembly using Oxford Nanopore Sequencing in combination with Illumina sequencing.

To build microPIPE we evaluated the performance of several tools at each step of bacterial genome assembly, including basecalling, assembly, and polishing. Results at each step were validated using the high-quality ST131 Escherichia coli strain EC958 (GenBank: HG941718.1). After appraisal of each step, we selected the best combination of ...