TALC: Transcript-level Aware Long-read Correction

Broseus, Lucile; Thomas, Aubin; Oldfield, Andrew; Séverac, Dany; Dubois, Emeric; Ritchie, William

doi:10.1093/bioinformatics/btaa634

Cited by 15 publications

(15 citation statements)

References 61 publications

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“…Raw sequence data were then base-called using Guppy v3.6.1. Once the raw signal from the MinION fast5 files was converted into fastq files, the sequencing errors were corrected using TALC v1.01 (74)(https://gitlab.igh.cnrs.fr/lbroseus/TALC) by using the Illumina short reads sequence of kuruma shrimp hemocytes (DDBJ Sequence Read Archive (DRA) accession number DRA004781). The corrected long-read sequences from MinION and short-read sequences from Illumina Miseq were hybrid de novo assembled using rnaSPAdes v3.14.1 (75)(https://cab.spbu.ru/software/rnaspades/) and Trinity 2.10.0 (76)(https://github.com/trinityrnaseq/trinityrnaseq/wiki).…”

Section: Methodsmentioning

confidence: 99%

Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process

Koiwai

Koyama

Tsuda³

et al. 2021

Preprint

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Crustacean aquaculture is expected to be a major source of fishery commodities in the near future. Hemocytes are key players of the immune system in shrimps; however, their classification, maturation, and differentiation are still under debate. To date, only discrete and inconsistent information on the classification of shrimp hemocytes has been reported, showing that the morphological characteristics are not sufficient to resolve their actual roles. Our present study using single-cell RNA sequencing, revealed nine types of hemocytes of Marsupenaeus japonicus based on their transcriptional profiles. We identified markers of each subpopulation and the differentiation pathways involved in their maturation. We also discovered cell growth factors that might play crucial roles in hemocyte differentiation. Different immune roles among these subpopulations were suggested from the analysis of differentially expressed immune-related genes. These results provide a unified classification of shrimp hemocytes, which improves the understanding of its immune system.

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Section: Methodsmentioning

confidence: 99%

Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process

Koiwai

Koyama

Tsuda³

et al. 2021

Preprint

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“…Direct RNA reads were corrected using TALC (version 1.0) [ 36 ] with default parameters (except -k = 21) and Illumina reads from leaf and root samples of B. napus downloaded from the EBI database (ERX397788 and ERX397800). Before the correction step, raw reads were masked using DustMasker (version 1.0.0 from the BLAST 2.10.0 package) [ 37 ], and we kept reads with ≥150 unmasked positions and ≥75% of unmasked bases.…”

Section: Introductionmentioning

confidence: 99%

Long-read assembly of the Brassica napus reference genome Darmor-bzh

et al. 2020

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Background The combination of long reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allows access to the gene catalogue of a given species but also reveals the architecture and organization of chromosomes, including complex regions such as telomeres and centromeres. The Brassica genus is not exempt, and many assemblies based on long reads are now available. The reference genome for Brassica napus, Darmor-bzh, which was published in 2014, was produced using short reads and its contiguity was extremely low compared with current assemblies of the Brassica genus. Findings Herein, we report the new long-read assembly of Darmor-bzh genome (Brassica napus) generated by combining long-read sequencing data and optical and genetic maps. Using the PromethION device and 6 flowcells, we generated ∼16 million long reads representing 93× coverage and, more importantly, 6× with reads longer than 100 kb. This ultralong-read dataset allows us to generate one of the most contiguous and complete assemblies of a Brassica genome to date (contig N50 > 10 Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes. Conclusion Using these cutting-edge technologies, and in particular by relying on all the advantages of the nanopore technology, we provide the most contiguous Brassica napus assembly, a resource that will be valuable to the Brassica community for crop improvement and will facilitate the rapid selection of agronomically important traits.

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“…However, a correction step results in more mapped reads and a better definition of the intronic boundaries. The most efficient approach for correcting long reads in transcriptomic data is to use short (second generation) sequencing reads of the same samples (Amarasinghe et al, 2020; Hackl, Hedrich, Schultz, & Förster, 2014). For reasonable runtimes, ease of implementation and good correction results, we recommend using either TALC (Broseus et al, 2020), LoRDEC (Salmela & Rivals, 2014) or CoLoRMap (Haghshenas, Hach, Sahinalp, & Chauve, 2016). It is worth noting that hybrid correction gives excellent results even with data sourced from different laboratories (Broseus et al, 2020).…”

Section: Computational Detection Of Irmentioning

confidence: 99%

Intron retention and its impact on gene expression and protein diversity: A review and a practical guide

et al. 2020

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Intron retention (IR) occurs when a complete and unspliced intron remains in mature mRNA. An increasing body of literature has demonstrated a major role for IR in numerous biological functions, including several that impact human health and disease. Although experimental technologies used to study other forms of mRNA splicing can also be used to investigate IR, a specialized downstream computational analysis is optimal for IR discovery and analysis. Here we provide a review of IR and its biological implications, as well as a practical guide for how to detect and analyze it. Several methods, including long read third generation direct RNA sequencing, are described. We have developed an R package, FakIR, to facilitate the execution of the bioinformatic tasks recommended in this review and a tutorial on how to fit them to users aims. Additionally, we provide guidelines and experimental protocols to validate IR discovery and to evaluate the potential impact of IR on gene expression and protein output. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Processing > Splicing Regulation/Alternative Splicing RNA Methods > RNA Analyses in vitro and In Silico K E Y W O R D S intron retention, nonsense mediated decay, post-transcriptional gene regulation, RNA export, RNA processing 1 | INTRODUCTION Alternative splicing of messenger RNA (mRNA) is responsible for much of the proteome complexity in mammals (Berget, Moore, & Sharp, 2000; Nilsen & Graveley, 2010). We now know that at least 90% of all mammalian genes can undergo some form of alternative splicing, often generating multiple protein isoforms with sometimes disparate biological functions (Wang et al., 2008). Intron retention (IR) is a type of alternative splicing that is gaining increased interest in human health and disease research. Originally described in plants and viruses, IR has now been shown to be a common form of alternative David F. Grabski, Lucile Broseus, and Bandana Kumari contributed equally to this study.

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TALC: Transcript-level Aware Long-read Correction

Cited by 15 publications

References 61 publications

Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process

Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process

Long-read assembly of the Brassica napus reference genome Darmor-bzh

Intron retention and its impact on gene expression and protein diversity: A review and a practical guide

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