Workflows
What is a Workflow?Filters
Snakemake workflow: Isoseq3.3
This workflow implements the PacBio Isoseq v3.3.0 pipeline.
Note: Currently this workflow is limited to non-multiplexed samples.
Authors
- Terry Bertozzi
Usage
If you use this workflow in a paper, don't forget to cite the URL of this (original) repository and, if available, its DOI (see above).
Step 1: Obtain a copy of this workflow
- Create ...
Assembly, visualisation and quality control workflow for high fidelity reads built from circular consensus sequence (PacBio HiFi) data.
Assembly, visualisation and quality control workflow for high fidelity reads built from circular consensus sequence (PacBio HiFi) data.
Assembly, visualisation and quality control workflow for high fidelity reads built from circular consensus sequence (PacBio HiFi) data.
SARS-CoV-2 Sequence Quality Assurance Workflow Kontraption, version 4.0.2
This workflow take as input a collection of paired fastq. It will remove bad quality and adapters with cutadapt. Map with Bowtie2 end-to-end. Will remove reads on MT and unconcordant pairs and pairs with mapping quality below 30 and PCR duplicates. Will compute the pile-up on 5' +- 100bp. Will call peaks and count the number of reads falling in the 1kb region centered on the summit. Will plot the number of reads for each fragment length.