PASA specifications


Unique identifier OMICS_20215
Alternative name Program to Assemble Spliced Alignments
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A targeted genome and some transcripts.
Input format FASTA
Operating system Unix/Linux, Mac OS
Programming languages C++, Perl
Computer skills Advanced
Version 2.1.0
Stability Stable
Source code URL
Maintained Yes


  • Invertebrates
    • Plasmodium falciparum
  • Plants and Fungi
    • Arabidopsis thaliana
    • Aspergillus fumigatus
    • Oryza sativa
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus



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  • person_outline Brian Haas <>

Publication for Program to Assemble Spliced Alignments

PASA institution(s)
J Craig Venter Institute, The Institute for Genomic Research, Rockville, MD, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Bioinformatics and Computational Biology, Department of Computer Science, University of Maryland, College Park, MD, USA; Computation Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA; Institute for Genome Sciences, University of Maryland Medical School, Baltimore, MD, USA; Department of Plant Biology, Michigan State University, East Lansing, MI, USA
PASA funding source(s)
Supported by a National Science Foundation Plant Genome Research Program grant (DBI-0321538); by NIH grant R01-LM006845 and by MSC contract NIH-N01-AI-30071.

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