awesome-sequencing-tech-papers

A collection of papers and preprints on comparison of long and/or short read sequencing technologies. |Sequencing|Technologies|For|The Win| |:--:|:--:|:--:|:--:| | 2021 (in progress) | 2020| 2019| 2018|

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

Contribute by submitting pull requests, or posting suggestions as issues. Thank you.

2021

Title: 🦠 High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing

Platforms: ONT and PacBio

2020

Title: 🧬 Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes

Platforms: ONT's PromethION, and PacBio RS II.

Title: 🧬 An Extensive Sequence Dataset of Gold-Standard Samples for Benchmarking and Development

Platforms: PacBio Sequel II System (Chemistry 2.0), and Illumina (NovaSeq, HiSeq4000, and HiSeqX)

Title: 🧬 Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

Description: "Assembly workflow that combines Strand-seq and long reads in a reference-free manner to provide fully phased and highly contiguous de novo assemblies of diploid human genomes"

Platforms: PacBio Sequel II (Chemistry v1), and PacBio RSII (P6-C4 Chemistry) and PacBio Sequel II (Chemistry 2.0) for BAC clone insert sequencing

Title: 📚 Sequencing platform shifts provide opportunities but pose challenges for combining genomic datasets

Description: Opinion article that highlights impact of Illumina's base calling for sequencing data produced with four-channel chemistry (e.g. HiSeqX) and two-channel chemistry (e.g. NextSeq and NovaSeq).

Title: 🦠 Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis

Platforms: ONT PromethION and Illumina MiSeq

Title: 🌱 Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacific Biosciences Sequel II system and ultralong reads of Oxford Nanopore

Description: Comparison of two assemblies of Oryza sativa (rice)

Platforms: ONT PromethION and PacBio Sequel II

Title: 🌱 Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements

Description: A combination of long-read sequencing and Hi-C technology to generate contiguous dikaryotic reference genome. See Table 1 for statistics.

Platforms: PacBio RSII (18 SMRT cells), PacBio Sequel (11 SMRT cells), Hi-C, and Illumina paired-end reads (125bp on HiSeq, 150bp on NextSeq 500).

Title: 🧬 Telomere-to-telomere assembly of a complete human X chromosome

Description: The study presents first ever gapless telomere-to-telomere assembly of human X chromosome, enabled by ultra-long reads.

Platforms: Illumina linked reads, 10X Genomics, PacBio (CLRs and HiFi Reads), ONT, and Hi-C.

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: 🧬 Benchmarking challenging small variants with linked and long reads

Description: Use of long and linked reads to expand Genome In A Bottle's benchmark in order to indentify regions such as segmental duplications.

Platforms: 10x Genomics, Complete Genomics, PacBio Sequel II, ONT.

Title: 🌲🍂 Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome

Description: Assessment of mitochondrial reads (using sequencing, assembly, and annotation) to study Siberian larch.

Platforms: Illumina (HiSeq 2000) and ONT (MinION).

Title: 🐟 Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American killifish from the Fundulus genus

Description: A study on a collection of whole genome data of killifish species obtained from ONT and Illumina platforms

Platforms: ONT PromethION, and Illumina platforms (HiSeq 4000 and NovaSeq)

Title: A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification

Description: Comparison of MinION and PacBio Sequel II for full-transcript discovery and quantification in GM12878 cell line. PacBio platform captured more as compared to direct-RNA performed by MinION, however PacBio data is prone to antisense transcript artifacts. PacBio Sequel II data was also compared with Illumina RNA-Seq data for expression levels.

Platforms: ONT MinION and PacBio Sequel II

Title: 🧬 Long-read human genome sequencing and its applications

Description: A review article that focuses on SMRT sequencing and ONT, and compare those two major long-read technologies with short-read sequencing platforms in terms of read accuracy, throughput, and cost.

Title: 📚 Opportunities and challenges in long-read sequencing data analysis

Description: An overview of the bioinformatics pipelines for nanopore and PacBio sequencing, with a focus on downstream analyses such as error correction, structural variant calling, and detection of base modifications.

Title: 🦠 A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes

Platforms: ONT's MinION (FLO-MAP R7.3 flowcell) and Illumina MiSeq (16S Metagenomic Sequencing kit, 2×300bp paired-end)

Title: 🦠 Benchmarking of long-read assemblers for prokaryote whole genome sequencing

Platforms: ONT MinION (R9.4), PacBio RSII (CLR), and Illumina (for hybrid assemblies)

Title: 🦁 Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data

Description: The study showed that data from 10x Genomics and Dovetai Hi-C were sufficient for chromosome genome assembly. For sequence fill-in (closing gaps between contigs with ambiguous sequence), nanopore data (MinION) was used. Besides quality of assembly and phylogenetic relationships of species taxa, the study reports how reference genome bias influences heterozygosity estimates across species.

Title: Long-read error correction: a survey and qualitative comparison

Description: A comprehensive analysis of 29 tools using PacBio and nanopore data.

Title: Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms

Description: Assessment of six long-read assembly algorithms for PacBio and ONT reads from a non-model non-vertebrate organism Adineta vaga

Title: 🇰🇷🧬 Comparative analysis of seven short-reads sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing

Description: Systematic comparison of a new whole-genome sequencer MGISEQ-T7 against Illumina short-read sequencers. The study concluded the MGI platform can be used for genomics research at nearly half the cost of the Illumina platforms.

Platforms: BGISEQ-500, MGISEQ-T7, HiSeq2000, HiSeq2500, HiSeq4000, HiSeqX10, and NovaSeq6000

Title: 🧬 Comprehensive analysis of structural variants in breast cancer genomes using single molecule sequencing

Description: Analysis of the SKBR3 breast cancer cell line and patient-derived organoids representing tumor and matching normal cells from two breast cancer patients.

Platforms: ONT MinION (R9.1 flow cell) , PacBio Sequel (SMRTbell template prep kit 1.0), Illumina (TruSeq RNA Library prep kit), and 10x Genomics

2019

Title: 🐭 & 🧬 Comparative analysis of sequencing technologies for single-cell transcriptomics

Platforms: BGISEQ-500 and Illumina (HiSeq2500 and HiSeq4000)

Title: 🇯🇵🧬 Construction and Integration of Three De Novo Japanese Human Genome Assemblies toward a Population-Specific Reference

Description: Construction of a reference genome using hybrid scaffolding approach by integrating de novo assemblies of three Japanese male individuals. BionanoSolve software (v3.2) was used for hybrid scaffolding.

Platforms: PacBio RSII (using P6-C4 chemistry), Illumina HiSeq 2500 system (with a TruSeq Rapid PE Cluster kit and Rapid SBS kit), and Irys/Saphyr system (BioNano Genomics) for optical mapping.

Title: 🇰🇷🧬 Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information

Description: The study concludes that "the pore-based PromethION approach provides a good quality chromosome-scale human genome assembly at a low cost and is much more cost-effective than PacBio."

Platforms: ONT PromethION R9.4.1, PacBio Sequel, Illumina HiSeq 2000, and Arima-HiC kit (A160105 v01)

Title: 📚💉🧬 Long-Read Sequencing Emerging in Medical Genetics

Description: A review article that discusses potential of long-read sequencing technologies in a context of advancements in medical genetics.

Title: 📚🧬 Long-read sequencing in deciphering human genetics to a greater depth

Description: A review article focused towards advantages and limitations of long-read sequencing

Title: 🦠 Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

Title: 🌱 A critical comparison of technologies for a plant genome sequencing project

Description: Comparison between Illumina short read, PacBio, 10x Genomics linked reads, Dovetail Hi-C, and BioNano optical maps for assembling high-quality potato species Solanum verrucosum. The comparison involves assessment of completeness, accuracy, requirements, and sequencing costs.

Title: Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV)

Title: Multi-platform discovery of haplotype-resolved structural variation in genomes

Title: 🧬 Sequencing of human genomes with nanopore technology

Description: The main focus of this study is the use of nanopore technology (MinION) for clinical use. In addition to evaluating performance of basecallers for SNV calls, the study also looked at comparison of large variants (>100bp) from read data generated by ONT, PacBio, and Illumina (section 3.2, supplementary).

2018

Title: 📚💉🧬 Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

Description: A summary of how SMRT sequencing technology has evolved into PacBio's RS II and Sequel systems and its use for various types of genetics studies.

Title: 📚💉🧬 Single-Molecule Sequencing: Towards Clinical Applications

Description: A nice review on how PacBio and ONTs are being used for microbiology, pharmacogenomics, cancer studies, and so on.

Title: 🦠 NGS Technologies and their Application to the Study and Control of Bacterial Infection

Title: 🦠 Targeted Long-Read Sequencing of a Locus Under Long-Term Balancing Selection in Capsella

Title: 🦠 Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices

Platforms: Illumina MiSeq and ONT MinION

Title: High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes

Contribute by submitting pull requests, or posting suggestions as issues. Thank you.