All Published Workflows
28 workflows that have been reviewed and published
Small collection of tools for performing quality control on coronavirus sequencing data and genomes
Tools and plots for perfoming quality control on coronavirus sequencing results. Download the package:
git clone https://gith...
A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.
A Snakemake workflow to process single samples (unrelated individuals) or cohort samples (related individuals) of paired-end ...
Workflow for Nanopore Sequencing of 10x single cell libraries
ScNapBar (single-cell Nanopore barcode demultiplexer) is a workflow to assign barcodes to long-read single-cell sequencing...
Snakemake pipeline for single-cell long-read sequencing
This documentation - with additional info - will be hosted here at some point
#clone
git clone --recursive https://github...
Benchmarking adapter and quality trimming tools
Original implementation by Brian Bushnell (2014):
http://seqanswers.com/forums/showthread.php?t=42776 The following tools are...
A Snakemake workflow for ecDNA detection in Nanopore or Illumina sequencing reads derived from DNA samples enriched for circular DNA.
A Snakemake workflow for ecDNA detection in Nanopore or Illumina sequencing reads derived from DNA samples enriched for circu...
Second workflow that takes the output of the guppy workflow to run fastqc and create a multiQC report. Then run Mothur for analysis.
This workflow takes the output from the GUPPY workflow and runs fastqc, multiqc, and mothur.
Hans Vasquez-Gross
Lucas...
FastQC and MultiQC Workflow for BaseSpace Data Merging and Quality Control
This workflow performs fastqc on an input PROJECT directory downloaded from basespace. It will merge the FASTQ files between ...
The repository host the snakemake file for 16S rRNA and shotgun sequencing data including QIIME2 and kraken2/bracken for 16S and metaphalan3 and kraken2/bracken for shotgun.
This is an ongoing project to generate a snakemake workflow to anlaysis 16S rRNA and shotgun seqeucnign microbial data using ...
A Snakemake workflow to basecall, quality control and assemble Nanopore data.
A Snakemake workflow to basecall, quality control and assemble Nanopore data.
taxonomic_profiling_pipeline
This pipeline was developed using the Snakemake workflow management system You would need to have the Snakefile, the en...
Snakemake workflow for microbiome research cluster analysis using fastp, Kraken2, and BIOM.
A Snakemake workflow to analyse long read human microbiome data with steps for general quality control and taxonomy assignmen...