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rnaSPAdes
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rnaSPAdes

rnaSPAdes is a de novo RNA-seq full-length transcriptome assembly tool. The rnaSPAdes extends the SPAdes genome assembler and can handle paired-end reads, isoforms, and multiple insert sizes.



rnaSPAdes

rnaSPAdes is a de novo RNA-seq full-length transcriptome assembly tool. The rnaSPAdes extends the SPAdes genome assembler and can handle paired-end reads, isoforms, and multiple insert sizes.

Topic

Transcriptomics; Sequence assembly; RNA-Seq

Details

  • Operation: Transcriptome assembly
  • Input: FASTA, FASTQ, BAM
  • Output: FASTQ, FASTA, GFA, .paths (assembly graph)
  • Software interface: Command-line user interface
  • Language: Python;Perl;C++
  • Operating system: Linux
  • License: GNU GPL v2
    • Cost: Free
  • Version name: 3.13.1
    • Maturity: Stable
  • Credit: The Russian Foundation for Basic Research, St. Petersburg State University.
  • Contact: spades.support _at_ cab.spbu.ru
  • Collection: -

Publications

Bushmanova E, Antipov D, Lapidus A, Prjibelski AD "rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data." Gigascience. 2019 Sep 1;8(9). pii: 5559527. https://doi.org/10.1093/gigascience/giz100
PMID: 31494669
PMCID: PMC6736328


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