Useful Links

AWS-specific

• AWS Batch workflow - Introduction
• AWS Batch workflow - github page
• SRAtoolkit in Cloud Computing
• NCBI SRA Data on S3
• S3 transfer optimization
• Paper on analyzing EC2 costs (2011)
• Pushing the limits of Amazon S3 Upload Performance
• Clever SRA alignment pipeline

SARS-CoV-2

• SARS-CoV-2 UCSC Genome Browser
• Interpretable detection of novel human viruses from genome sequencing data
• Virus detection from RNA-seq: proof of concept
• Potential Host Range for SARS-CoV-2

Bloom Filters

• Bigsi: Bloom filter indexing of SRA/ENA for organism search
• Fast Search of Thousands of Short-Read Sequencing Experiments
• Ultra-fast search of all deposited bacterial and viral genomic data