Concepedia

Short-read Transcriptome Assembly

Short-Read Transcriptome Assembly is a computational method in transcriptomics that reconstructs full-length transcripts from high-throughput sequencing reads of length typically under 300 nucleotides, distinguished by its reliance on short RNA-seq reads as the primary input for de novo or reference-guided assembly.

34

Publications

7.5K

Citations

194

Authors

91

Institutions

Publications per year

2017–2026

15

Parents

Publications

34

Transcriptome assembly from long-read RNA-seq alignments with StringTie2

Sam Kovaka, Aleksey V. Zimin, Geo Pertea et al. · Genome biology · 2019 · 2.1K citations · Full text

, , +17

SOAPdenovo-Trans: <i>de novo</i> transcriptome assembly with short RNA-Seq reads

Yinlong Xie, Gengxiong Wu, Jingbo Tang et al. · Bioinformatics · 2014 · 998 citations · Full text

, , +12

rnaSPAdes: a <i>de novo</i> transcriptome assembler and its application to RNA-Seq data

Elena Bushmanova, Dmitry Antipov, Alla Lapidus et al. · GigaScience · 2019 · 900 citations · Full text

, , +15

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

Qiongyi Zhao, Yi Wang, Yimeng Kong et al. · BMC Bioinformatics · 2011 · 486 citations · Full text

, , +16

Improved transcriptome assembly using a hybrid of long and short reads with StringTie

Alaina Shumate, Brandon Wong, Geo Pertea et al. · PLoS Computational Biology · 2022 · 480 citations · Full text

, , +17

1–5 of 34

Authors

194

  1. GP
    Geo Pertea

    Johns Hopkins University, United States

    4 publications · 2.7K citations

    4

    h-index

  2. MP
    Mihaela Pertea

    Johns Hopkins University, United States

    4 publications · 2.7K citations

    4

    h-index

  3. AD
    Andrey D. Prjibelski

    St Petersburg University, Russia

    3 publications · 965 citations

    3

    h-index

  4. EB
    Elena Bushmanova

    St Petersburg University, Russia

    3 publications · 965 citations

    3

    h-index

  5. AL
    Alla Lapidus

    Joint Genome Institute, United States

    2 publications · 931 citations

    2

    h-index

1–5 of 194

Institutions

91

  1. Johns Hopkins University

    Baltimore, United States

    4 h-index

    18 publications

    14.8K citations

  2. University of Washington

    Seattle, United States

    3 h-index

    7 publications

    340 citations

  3. St Petersburg University

    Saint Petersburg, Russia

    3 h-index

    10 publications

    3.8K citations

  4. University of Hong Kong

    Pok Fu Lam, Hong Kong

    2 h-index

    19 publications

    16.2K citations

  5. South China University of Technology

    Guangzhou, China

    2 h-index

    17 publications

    16K citations

  6. Lieber Institute for Brain Development

    Baltimore, United States

    2 h-index

    2 publications

    495 citations

  7. Central South University

    Changsha, China

    2 h-index

    17 publications

    16K citations

  8. Chinese Academy of Sciences

    Beijing, China

    2 h-index

    7 publications

    1.7K citations

1–8 of 91

Venues

  1. PLoS ONE

    4 publications · 173 citations

    4

    h-index

  2. BMC Genomics

    4 publications · 548 citations

    4

    h-index

  3. bioRxiv (Cold Spring Harbor Laboratory)

    Repository · 3 publications · 155 citations

    3

    h-index

  4. GigaScience

    3 publications · 1.2K citations

    3

    h-index

  5. arXiv (Cornell University)

    Repository · 1 publications · 72 citations

    1

    h-index

1–5