Introduction to Bioinformatics workflows with Nextflow and nf-core
Getting Started with Nextflow
Objectives Understand
What a workflow management system is.
Understand the benefits of using a workflow management system.
Explain the benefits of...
KeyDescription
F1
Yes! Read it first. BTW, FarEng.hlf is a simple text file, you can open it in any editor.
ShiftF1
Create new archive from selected files
ShiftF2
Extract files from selected...
The US government SARS-CoV-2 Interagency Group (SIG) developed a Variant Classification scheme that defines three classes of SARS-CoV-2 variants:
Variant of Interest
Variant of Concern
Variant of High Consequence
Intersting...
The pipeline was developed based on a popular workflow framework Nextflow, composed of four core procedures including reads alignment, assembly, identification and quantification. It contains various unique features such as well-designed...
Resource for downloading all the HISAT2 related files
Please cite:
Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915...
The ENCODE project uses Reference Genomes from NCBI or UCSC to provide a consistent framework for mapping high-throughput sequencing data. In general, ENCODE data are mapped consistently to 2 human (GRCH38, hg19) and 2 mouse...
We aim to provide readers with a gentle introduction to a few key machine learning techniques, including the most recently developed and widely used techniques involving deep neural networks. We describe how different techniques may be suited to...
RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include:
Homology-based misassembly correction
Homology-based assembly scaffolding and patching
Scaffold merging