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.