Key:

Hi-C, chromosome conformation capture
ONT, Oxford Nanopore Technology
PacBio, Pacific Biosciences
- SMRT, Single-Molecule Real-Time
- CLR, Continuous Long Read
- CCS, Circular Consensus Sequencing
- Hi-Fi, High-Fidelity
📚 Review/Opinion Article
🧬 Study involves human genome(s)
🦠 Prokaryotic genome(s)
🌱 Plant genome(s)
💉 Focused towards medical genetics
🛠 Includes tool/software development

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2021

Title: 🛠 🧬 Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks

Description: Evaluation of variant calling performance and runtime comparison of haplotype-aware pipelines

Platforms: The study used the HG003 and HG004 samples (from PrecisionFDA); analysing the 35X coverage of Illumina NovaSeq reads, 35X PacBio HiFi, and 90X ONT.

Title: 🌱 Combined use of Oxford Nanopore and Illumina sequencing yields insights into soybean structural variation biology

Description: The study is about exploring structural variants (SVs) in soybean's transposable element (TE) . The authors developed a pipeline to find whether SVs at various sites were due to novel TE insertion and/or excision.

Platforms: ONT MinION (SQK-LSK109 genomic DNA ligation kit) with a FLO-MIN106D flowcell (R9 chemistry), and Illumina HiSeq 2500

Title: 🦠 Microbial metagenome-assembled genomes of the Fram Strait from short and long read sequencing platforms

Platforms: Comparison was performed on datasets from marine environmental samples usinng PacBio Sequel II and Illumina HiSeq 3000.

Title: 🦠 Benchmarking metagenomic classification tools for long-read sequencing data

Platforms: ONT and PacBio - See section 2.2 Test Datasets for information on data sources.

Title: 🧬 Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome

Platforms: Comparison was performed between data from Illumina Human BodyMap 2.0 Project and PacBio Sequel II

Title: 🦠😛 High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes

Description: The study involves samples from human tongue.

Platforms: Illumina MiSeq and NextSeq500 and ONT's MinION

Title: 🧬 Targeted long-read sequencing identifies missing disease-causing variation

Description: Use of adaptive sampling via ONT and PacBio platforms

Platforms: ONT's GridION (with MinKNOW control software v18.04.1), PacBio CLR sequencing (SMRT Cell 1Ms on the Sequel platform using v3 chemistry), and PacBio HiFi sequencing (SMRT Cell 8M on a Sequel II instrument)