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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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)
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
Description: Comparison of two assemblies of Oryza sativa (rice)
Platforms: ONT PromethION and PacBio Sequel II
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 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.
Description: Assessment of mitochondrial reads (using sequencing, assembly, and annotation) to study Siberian larch.
Platforms: Illumina (HiSeq 2000) and ONT (MinION).
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.
Platforms: ONT's MinION (FLO-MAP R7.3 flowcell) and Illumina MiSeq (16S Metagenomic Sequencing kit, 2×300bp paired-end)
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
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
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