SOP_data

Standard Operating Procedures

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Data and Code SOPs

General Procedures

• Coding Best Practices
• Electronic Lab Noteboooks
• How to Create an SOP

Data deposition

• Depositing Data in NCBI - including BioProject, BioSample, Genome, and SRA deposition
• Data retrieval from public databases

Genome Analysis

Before annotating or assembling it is a good idea to start the BioSample and BioProject (once you know the sample is clean)

• Fungal Genome_Assembly_with_Illumina_Reads
• Fungal Genome annotation
• Hybrid Assembly
• Contamination assessment

Amplicon Analysis

• UCR HPCC AMPtk amplicon (microbiome) analysis
• 16S Bacteria and Archaea
• ITS Fungal

Metagenome assembly and analysis

• KBase Metagenomes Analysis
• UCR HPCC Metagenomes Analysis
  • Data cleaning
  • Metagenome Assembly
  • Metagenome annotation and Analysis

Viral metagnomics

• KBase Viral Analysis
• UCR HPCC Cluster Viral Analysis

Phylogenomics

• PHYling phylogenomics

Transcriptome

• Trinity RNA-seq Assembly

Vizualization

• JBrowse