nazeeefa / awesome-sequencing-tech-papers

A collection of publications on comparison of high-throughput sequencing technologies.

awesome-sequencing-tech-papers

A collection of papers on comparison of long and/or short read sequencing technologies (and data generated from the platforms).

Sequencing	Technologies	For	The	Win
2024, 2023	2022, 2021	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
• 🛠 Includes tool/software development

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

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2024

Title: Genome-wide profiling of highly similar paralogous genes using HiFi sequencing

Title: The Hitchhiker’s Guide to Sequencing Data Types and Volumes for Population-Scale Pangenome Construction

Title: A graph clustering algorithm for detection and genotyping of structural variants from long reads

2023

Title: Primed and ready: Nanopore metabarcoding can now recover highly accurate consensus barcodes that are generally indel-free

Description: Sequencing of zooplankton samples to recover molecular operational taxonomic units (MOTUs). At the sample-level, Illumina metabarcoding recovered more MOTUs than nanopore.

Platforms: Illumina MiSeq and ONT's minION (R10.3 chemistry)

Title: Performance analysis of conventional and AI-based variant callers using short and long reads

Platforms: Illumina HiSeq2500

Title: The long and short of it: Benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies

Description: Assessment of assembly algorithms for the analysis of viromes (mock community of 15 bacteriophage genomes), and assessment of error rates across different platforms.

Platforms: Illumina MiSeq (NexteraXT library prep kit), minION (library prep by SQK-LSK109), and PacBio Sequel.

2022

Title: Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore reveals platform-specific error patterns

Description: Isoform analysis of mouse data via sequencing cDNA of reverse transcription events.

Platforms: PacBio Sequel II, and ONT PromethION

Title: 🧬 Target enrichment long-read sequencing with adaptive sampling can determine the structure of the small supernumerary marker chromosomes

Description: Comparative analysis of two clinical samples

Platforms: HiSeq 1500 (2 × 101 bp) and, ONT's GridION using R9.4.1 flowcell (ligation sequencing kit SQK-LSK109)

Title: 🧬 An assessment of bioinformatics tools for the detection of human endogenous retroviral insertions in short-read genome sequencing data

Description: Analysis of 50 human endogenous retroviruses (HERVs) short-read whole-genome sequences, "matching long and short read data, and simulated short-read data."

Platforms: Illumina HiSeq 2000 and 2500, and PacBio Sequel

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

awesome-sequencing-tech-papers's Issues

Is this paper relevant?

Heya, how about https://www.nature.com/articles/s41467-019-09637-5?

It is an indirect comparison to short read sequencing through the evaluation of SNP calling quality.

From the paper:

Abstract
Whole-genome sequencing (WGS) is becoming widely used in clinical medicine in diagnostic contexts and to inform treatment choice. Here we evaluate the potential of the Oxford Nanopore Technologies (ONT) MinION long-read sequencer for routine WGS by sequencing the reference sample NA12878 and the genome of an individual with ataxia-pancytopenia syndrome and severe immune dysregulation. We develop and apply a novel reference panel-free analytical method to infer and then exploit phase information which improves single-nucleotide variant (SNV) calling performance from otherwise modest levels. In the clinical sample, we identify and directly phase two non-synonymous de novo variants in SAMD9L, (OMIM #159550) inferring that they lie on the same paternal haplotype. Whilst consensus SNV-calling error rates from ONT data remain substantially higher than those from short-read methods, we demonstrate the substantial benefits of analytical innovation. Ongoing improvements to base-calling and SNV-calling methodology must continue for nanopore sequencing to establish itself as a primary method for clinical WGS.

Disclaimer: A friend of mine is an author on this paper.