Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 70,170 bioRxiv papers from 306,408 authors.

Scallop Enables Accurate Assembly Of Transcripts Through Phasing-Preserving Graph Decomposition

By Mingfu Shao, Carl Kingsford

Posted 03 Apr 2017
bioRxiv DOI: 10.1101/123612 (published DOI: 10.1038/nbt.4020)

We introduce Scallop, an accurate, reference-based transcript assembler for RNA-seq data. Scallop significantly improves reconstruction of multi-exon and lowly expressed transcripts. On 10 human samples aligned with STAR, Scallop produces (on average) 35.7% and 37.5% more correct multi-exon transcripts than two leading transcript assemblers, StringTie and TransComb, respectively. For transcripts expressed at low levels in the same samples, Scallop assembles 65.2% and 50.2% more correct multi-exon transcripts than StringTie and TransComb, respectively. Scallop obtains this improvement through a novel algorithm that we prove preserves all phasing paths from reads (including paired-end reads), while also producing a parsimonious set of transcripts and minimizing coverage deviation.

Download data

  • Downloaded 1,355 times
  • Download rankings, all-time:
    • Site-wide: 4,948 out of 70,177
    • In bioinformatics: 946 out of 6,878
  • Year to date:
    • Site-wide: 56,629 out of 70,177
  • Since beginning of last month:
    • Site-wide: 45,283 out of 70,177

Altmetric data

Downloads over time

Distribution of downloads per paper, site-wide


Sign up for the Rxivist weekly newsletter! (Click here for more details.)