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Establishing evidenced-based best practice for the de novo assembly and evaluation of transcriptomes from non-model organisms

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/s11033-013-2667-3openalex-snapshot

Transcriptome profiling and digital gene expression analysis of Nile tilapia (Oreochromis niloticus) infected by Streptococcus agalactiae

inferredcites →https://doi.org/10.1016/j.gene.2015.03.070openalex-snapshot

Gene cloning, characterization and expression and enzymatic activities related to trehalose metabolism during diapause of the onion maggot Delia antiqua (Diptera: Anthomyiidae)

inferredcites →https://doi.org/10.1016/j.tree.2004.11.017openalex-snapshot

Candidate genes for behavioural ecology

inferredcites →https://doi.org/10.1038/nature12270openalex-snapshot

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming

inferredcites →https://doi.org/10.1038/ng.1028openalex-snapshot

De novo assembly and genotyping of variants using colored de Bruijn graphs

inferredcites →https://doi.org/10.1038/nmeth.1613openalex-snapshot

Computational methods for transcriptome annotation and quantification using RNA-seq

inferredcites →https://doi.org/10.1038/nprot.2013.084openalex-snapshot

De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity

inferredcites →https://doi.org/10.1073/pnas.1121464109openalex-snapshot

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

inferredcites →https://doi.org/10.1073/pnas.1320101110openalex-snapshot

Characterization of the human ESC transcriptome by hybrid sequencing

inferredcites →https://doi.org/10.1093/bib/bbq020openalex-snapshot

De novo assembly of short sequence reads

inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot

edgeR : a Bioconductor package for differential expression analysis of digital gene expression data

inferredcites →https://doi.org/10.1093/bioinformatics/btu030openalex-snapshot

BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads

inferredcites →https://doi.org/10.1093/bioinformatics/btu077openalex-snapshot

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/bioinformatics/btv290openalex-snapshot

BFC: correcting Illumina sequencing errors

inferredcites →https://doi.org/10.1093/bioinformatics/btv351openalex-snapshot

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

inferredcites →https://doi.org/10.1093/nar/29.13.2850openalex-snapshot

Genome-wide detection of alternative splicing in expressed sequences of human genes

inferredcites →https://doi.org/10.1093/nar/gkt215openalex-snapshot

Probabilistic error correction for RNA sequencing

inferredcites →https://doi.org/10.1101/021626openalex-snapshot

TransRate: reference free quality assessment of de-novo transcriptome assemblies

inferredcites →https://doi.org/10.1101/gr.126953.111openalex-snapshot

Efficient de novo assembly of large genomes using compressed data structures

inferredcites →https://doi.org/10.1101/gr.196469.115openalex-snapshot

TransRate: reference-free quality assessment of de novo transcriptome assemblies

inferredcites →https://doi.org/10.1111/1755-0998.12109openalex-snapshot

Principles of transcriptome analysis and gene expression quantification: an RNA ‐seq tutorial

inferredcites →https://doi.org/10.1111/j.1755-0998.2011.03024.xopenalex-snapshot

Field guide to next‐generation DNA sequencers

inferredcites →https://doi.org/10.1111/mec.12014openalex-snapshot

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA ‐seq experiments

inferredcites →https://doi.org/10.1126/science.1090100openalex-snapshot

Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays

inferredcites →https://doi.org/10.1186/1471-2105-11-485openalex-snapshot

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

inferredcites →https://doi.org/10.1186/1471-2105-15-182openalex-snapshot

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

inferredcites →https://doi.org/10.1186/1471-2164-14-146openalex-snapshot

De novo assembly and characterization of Camelina sativatranscriptome by paired-end sequencing

inferredcites →https://doi.org/10.1186/2047-217x-2-10openalex-snapshot

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

inferredcites →https://doi.org/10.1186/s13059-014-0509-9openalex-snapshot

Lighter: fast and memory-efficient sequencing error correction without counting

inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

inferredcites →https://doi.org/10.1186/s13059-014-0553-5openalex-snapshot

Evaluation of de novo transcriptome assemblies from RNA-Seq data

inferredcites →https://doi.org/10.1186/s13742-015-0089-yopenalex-snapshot

Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads

inferredcites →https://doi.org/10.12688/f1000research.6924.1openalex-snapshot

The khmer software package: enabling efficient nucleotide sequence analysis

inferredcites →https://doi.org/10.1371/journal.pone.0045524openalex-snapshot

The Social Brain: Transcriptome Assembly and Characterization of the Hippocampus from a Social Subterranean Rodent, the Colonial Tuco-Tuco (Ctenomys sociabilis)

inferredcites →https://doi.org/10.1371/journal.pone.0085182openalex-snapshot

A Snapshot of a Coral “Holobiont”: A Transcriptome Assembly of the Scleractinian Coral, Porites, Captures a Wide Variety of Genes from Both the Host and Symbiotic Zooxanthellae

inferredcites →https://doi.org/10.1371/journal.pone.0092598openalex-snapshot

Transcriptome Analysis of Salt Tolerant Common Bean (Phaseolus vulgaris L.) under Saline Conditions

inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot

Cutadapt removes adapter sequences from high-throughput sequencing reads

inferredcites →https://doi.org/10.1534/genetics.105.053611openalex-snapshot

Molecular Evolution and Population Genetic Analysis of Candidate Female Reproductive Genes in Drosophila

inferredcites →https://doi.org/10.3389/fgene.2014.00013openalex-snapshot

On the optimal trimming of high-throughput mRNA sequence data

inferredcites →https://doi.org/10.48550/arxiv.1203.4802openalex-snapshot

A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data

inferredcites →https://doi.org/10.48550/arxiv.1303.2223openalex-snapshot

khmer: Working with Big Data in Bioinformatics

inferredcites →https://doi.org/10.48550/arxiv.1505.02710openalex-snapshot

Near-optimal RNA-Seq quantification

inferredcites →https://doi.org/10.7717/peerj.113openalex-snapshot

Improving transcriptome assembly through error correction of high-throughput sequence reads

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/ajb2.1056openalex-snapshot

Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)

inferred← citeshttps://doi.org/10.1016/j.cbd.2019.03.005openalex-snapshot

Molecular physiology of copepods - from biomarkers to transcriptomes and back again

inferred← citeshttps://doi.org/10.1016/j.gene.2020.144765openalex-snapshot

Multi-species transcriptomics reveals evolutionary diversity in the mechanisms regulating shrimp tail muscle excitation-contraction coupling

inferred← citeshttps://doi.org/10.1016/j.margen.2016.11.002openalex-snapshot

Next generation sequencing of gonadal transcriptome suggests standard maternal inheritance of mitochondrial DNA in Eurhomalea rufa (Veneridae)

inferred← citeshttps://doi.org/10.1016/j.yhbeh.2017.11.011openalex-snapshot

Sex-biased transcriptomic response of the reproductive axis to stress

inferred← citeshttps://doi.org/10.1038/s41467-019-08891-xopenalex-snapshot

Dynamic pigmentary and structural coloration within cephalopod chromatophore organs

inferred← citeshttps://doi.org/10.1038/s41598-017-09334-7openalex-snapshot

De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)

inferred← citeshttps://doi.org/10.1038/s41598-018-31148-4openalex-snapshot

De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome

inferred← citeshttps://doi.org/10.1038/srep42110openalex-snapshot

Blubber transcriptome response to acute stress axis activation involves transient changes in adipogenesis and lipolysis in a fasting-adapted marine mammal

inferred← citeshttps://doi.org/10.1038/srep45125openalex-snapshot

Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic–pituitary–gonadal (HPG) axis

inferred← citeshttps://doi.org/10.1073/pnas.2313999120openalex-snapshot

A Na pump with reduced stoichiometry is up-regulated by brine shrimp in extreme salinities

inferred← citeshttps://doi.org/10.1093/jhered/esw044openalex-snapshot

Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals

inferred← citeshttps://doi.org/10.1093/jhered/esy001openalex-snapshot

Urban Evolutionary Ecology and the Potential Benefits of Implementing Genomics

inferred← citeshttps://doi.org/10.1093/jxb/erz114openalex-snapshot

Water stress combined with sulfur deficiency in pea affects yield components but mitigates the effect of deficiency on seed globulin composition

inferred← citeshttps://doi.org/10.1093/molbev/msx293openalex-snapshot

Female Mimicry by Sneaker Males Has a Transcriptomic Signature in Both the Brain and the Gonad in a Sex-Changing Fish

inferred← citeshttps://doi.org/10.1101/085365openalex-snapshot

Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic–pituitary–gonadal (HPG) axis

inferred← citeshttps://doi.org/10.1101/2021.09.16.460688openalex-snapshot

Comparative transcriptomics of seven Impatiens species

inferred← citeshttps://doi.org/10.1101/256875openalex-snapshot

Transcriptomic analyses reveal tissue-specific selection on genes related to apoptotic processes in the subterranean rodent, Ctenomys sociabilis

inferred← citeshttps://doi.org/10.1101/280420openalex-snapshot

De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp ( Penaeus monodon ) transcriptome

inferred← citeshttps://doi.org/10.1111/tpj.14008openalex-snapshot

Comparative RNA ‐seq analysis of nickel hyperaccumulating and non‐accumulating populations of Senecio coronatus (Asteraceae)

inferred← citeshttps://doi.org/10.1152/ajprenal.00067.2017openalex-snapshot

Severe acute dehydration in a desert rodent elicits a transcriptional response that effectively prevents kidney injury

inferred← citeshttps://doi.org/10.1186/s12864-017-3840-1openalex-snapshot

Characterizing the reproductive transcriptomic correlates of acute dehydration in males in the desert-adapted rodent, Peromyscus eremicus

inferred← citeshttps://doi.org/10.1186/s12870-019-1893-9openalex-snapshot

Mapping non-host resistance to the stem rust pathogen in an interspecific barberry hybrid

inferred← citeshttps://doi.org/10.12688/f1000research.8798.1openalex-snapshot

search.bioPreprint: a discovery tool for cutting edge, preprint biomedical research articles

inferred← citeshttps://doi.org/10.1371/journal.pone.0201206openalex-snapshot

An annotated CNS transcriptome of the medicinal leech, Hirudo verbana: De novo sequencing to characterize genes associated with nervous system activity

inferred← citeshttps://doi.org/10.1371/journal.pone.0243853openalex-snapshot

Quick and efficient approach to develop genomic resources in orphan species: Application in Lavandula angustifolia

inferred← citeshttps://doi.org/10.14264/uql.2017.487openalex-snapshot

Improving the Reproductive Performance of Domesticated Giant Tiger Shrimp, Penaeus monodon

inferred← citeshttps://doi.org/10.1534/g3.118.200992openalex-snapshot

Understanding the Loss of Maternal Care in Avian Brood Parasites Using Preoptic Area Transcriptome Comparisons in Brood Parasitic and Non-parasitic Blackbirds

inferred← citeshttps://doi.org/10.17760/d20316340openalex-snapshot

Elucidating the role of nanostructured pigment granules in the dynamic coloration of cephalopods

inferred← citeshttps://doi.org/10.3389/fevo.2021.659360openalex-snapshot

The Significance of Genotypic Diversity in Coral Competitive Interaction: A Transcriptomic Perspective

inferred← citeshttps://doi.org/10.3389/fmicb.2018.01581openalex-snapshot

Application of Transcriptomics to Compare the Carbohydrate Active Enzymes That Are Expressed by Diverse Genera of Anaerobic Fungi to Degrade Plant Cell Wall Carbohydrates

inferred← citeshttps://doi.org/10.3389/fpls.2021.720670openalex-snapshot

Genomic Resources to Guide Improvement of the Shea Tree

inferred← citeshttps://doi.org/10.3390/ijms21113872openalex-snapshot

Transcriptome Analysis of Maternal Gene Transcripts in Unfertilized Eggs of Misgurnus anguillicaudatus and Identification of Immune-Related Maternal Genes

inferred← citeshttps://doi.org/10.64898/2025.12.27.696710openalex-snapshot

Virome of Culex nigripalpus at an Alabama aquaculture site reveals diverse insect-specific viruses and the impact of dual bioinformatic pipelines

inferred← citeshttps://doi.org/10.70675/7f709739z9922z41f7z9144zdf4e76b0462bopenalex-snapshot

Bioinformatique pour l’exploration de la diversité inter-espèces et inter-populations : hétérogénéité & données multi-omiques

inferred← citeshttps://doi.org/10.7287/peerj.5428v0.1/reviews/1openalex-snapshot

Peer Review #1 of "The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly (v0.1)"

inferred← citeshttps://doi.org/10.7287/peerj.5428v0.1/reviews/2openalex-snapshot

Peer Review #2 of "The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly (v0.1)"

inferred← citeshttps://doi.org/10.7287/peerj.5428v0.1/reviews/3openalex-snapshot

Peer Review #3 of "The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly (v0.1)"

inferred← citeshttps://doi.org/10.7287/peerj.5428v0.2/reviews/1openalex-snapshot

Peer Review #1 of "The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly (v0.2)"

inferred← citeshttps://doi.org/10.7287/peerj.5428v0.2/reviews/2openalex-snapshot

Peer Review #2 of "The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly (v0.2)"

inferred← citeshttps://doi.org/10.7717/peerj.2617openalex-snapshot

Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse)

inferred← citeshttps://doi.org/10.7717/peerj.5428openalex-snapshot

The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly

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