Predicting Genes in Closely Related Species with Scipio and WebScipio

Kollmar, Martin

doi:10.1007/978-1-4939-9173-0_11

Cited by 2 publications

(3 citation statements)

References 25 publications

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“…Popular tools for de novo gene prediction including Augustus [28], GlimmerHMM [29], GeneID [30], Genscan [31], SNAP [32] and GeneMark-ES [33]. Popular homology-based methods include Genomix [34], AUGUSTUS [35], GeMoMa [36], Scipio and WebScipio [37], and OMGene [35]. Popular RNA-seq data-based methods include Braker2 [38], CAARs [39] and FINDER [40].…”

Section: Introductionmentioning

confidence: 99%

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User-friendly genome assembly and gene annotation pipelines for vertebrates

Wu,

Yuan,

2024

Preprint

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High-quality genome assembly and accurate gene annotation are critical to understand the biology and evolutionary history of a species. With the advance in sequencing technologies, assembling large vertebrate genomes using a combination of low-costing short reads and noisy long reads is in the reach of an individual lab. Although many tools have been developed, no single one is able to produce a chromosome-level assembly. Instead, a pipeline involving multiple steps using different tools is needed to achieve the goal. Nonetheless, it is difficult for a newcomer to choose an appropriate tool for each stage of pipeline and their combination for optimal performance. Moreover, most existing gene annotation tools cannot sufficiently and accurately identify both protein-coding genes and pseudogenes. Although gene annotation pipelines have been described such as those by NCBI and ENSEMBL, they are not available for individual labs due to the complexity of their use and required computational resources. To overcome these obstacles, here, we introduce user-friendly optimized genome assembly and gene annotation pipelines for vertebrates. Our genome assembly pipeline is able to produce chromosome-level assemblies with high quality using a combination of PacBio/Nanopore long reads, Illumina short reads and Hi-C short reads, and our gene annotation pipeline can accurately and sufficiently annotate both protein-coding genes and pseudogenes in an assembled genome using a combination of homology-based and RNA-seq data-based methods. Both pipelines show superior performances to existing ones in applications.

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Section: Introductionmentioning

confidence: 99%

“…Popular homology-based methods include Genomix [34], AUGUSTUS [35], GeMoMa [36], Scipio and WebScipio [37], and OMGene [35]. Popular RNA-seq data-based methods include Braker2 [38], CAARs [39] and FINDER [40].…”

Section: Introductionmentioning

confidence: 99%

User-friendly genome assembly and gene annotation pipelines for vertebrates

Wu,

Yuan,

2024

Preprint

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“…Tools for annotating the location and identity of TEs within a genome are a basic aspect of genomics, even where there is little ultimate research focus on TE biology. A key example is the assembly of a new genome, where TE annotation is performed so that TEs do not interfere with gene prediction pipelines (Campbell et al 2014; Kollmar 2019). This involves screening for TEs present in the genome and masking them, so they are filtered out during subsequent steps, typically using annotations that replace their nucleotide sequences with either lowercase letters (softmasking), or another symbol such as ‘N’ or ‘X’ (hardmasking).…”

Section: Introductionmentioning

confidence: 99%

Earl Grey: a fully automated user-friendly transposable element annotation and analysis pipeline

Baril

Imrie

Hayward

2022

Preprint

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Background: Transposable elements (TEs) are found in nearly all eukaryotic genomes and are implicated in a range of evolutionary processes. Despite considerable research attention on TEs, their annotation and characterisation remain challenging, particularly for non-specialists. Current methods of automated TE annotation are subject to several issues that can reduce their overall quality: (i) fragmented and overlapping TE annotations may lead to erroneous estimates of TE count and coverage; (ii) repeat models may represent small proportions of their total length, where 5' and 3' regions are poorly captured; (iii) resultant libraries may contain redundancy, with the same TE family represented more than once. Existing pipelines can also be challenging to install, run, and extract data from. To address these issues, we present Earl Grey: a fully automated transposable element annotation pipeline designed for the user-friendly curation and annotation of TEs in eukaryotic genome assemblies. Results: Using a simulated genome, three model genome assemblies, and three non-model genome assemblies, Earl Grey outperforms current widely used TE annotation methodologies in ameliorating the issues mentioned above by producing longer TE consensus sequences in non-redundant TE libraries, which are then used to produce less fragmented TE annotations without the presence of overlaps. Earl Grey scores highly in benchmarking for TE annotation (MCC: 0.99) and classification (97% correctly classified) in comparison to existing software. Conclusions: Earl Grey provides a comprehensive and fully automated TE annotation toolkit that provides researchers with paper-ready summary figures and outputs in standard formats compatible with other bioinformatics tools. Earl Grey has a modular format, with great scope for the inclusion of additional modules focussed on further quality control aspects and tailored analyses in future releases.

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Predicting Genes in Closely Related Species with Scipio and WebScipio

Cited by 2 publications

References 25 publications

User-friendly genome assembly and gene annotation pipelines for vertebrates

User-friendly genome assembly and gene annotation pipelines for vertebrates

Earl Grey: a fully automated user-friendly transposable element annotation and analysis pipeline

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