PASA protocols

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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 in pipelines

PMCID: 5282741
PMID: 28143409
DOI: 10.1186/s12864-017-3505-0

[…] scale. this is the first time this has been performed in these eukaryotic species., an initial de novo transcriptome assembly was generated by trinity for each species and then refined with program to assemble spliced alignments (pasa). the completeness and quality were assessed with the benchmarking universal single-copy orthologs (busco) and transrate tools at each stage […]

PMCID: 5414199
PMID: 28464849
DOI: 10.1186/s12864-017-3720-8

[…] using trinity []. existing munich information centre for protein sequences (mips) gene models were updated to include 5’ and 3’ utrs, alternative splice isoforms, and gene model fusions using the program to assemble spliced alignments (pasa; []). predicted gene models were categorized by cufflinks cuffcompare (‘e’ = possible pre-mrna fragment; ‘i’ = transfrag entirely within reference intron; […]

PMCID: 5824900
PMID: 29036429
DOI: 10.1093/dnares/dsx038

[…] were pooled together for de novo assembly using trinity with default parameters., to build a comprehensive transcriptome, the id accessions of full-length and de novo transcripts were first fed into pasa, and full-length, genome-guided and de novo transcripts generated in parallel were then collapsed, mapped back to fvb, and reconstructed by pasa through its alignment assembly module. […]

PMCID: 5266360
PMID: 28095660
DOI: 10.3347/kjp.2016.54.6.751

[…] and obtained distinct results in our draft genome of t. canis. in this study, we used more recent versions or new tools as follows: jellyfish, soapec, and gatk for sequencing; repeatrunner, maker, pasa, and blast2go for structural annotation. these results may be able to provide insights into the taxonomy of t. canis, host-parasite interactions, drug development, treatment protocols, […]

PMCID: 5266360
PMID: 28095660
DOI: 10.3347/kjp.2016.54.6.751

[…] structural annotation, homology search, functional annotation, classification of protein domains, and kegg pathway analysis were carried out. besides them, recently developed tools such as maker, pasa, evidence modeler, and blast2go were used. the scaffold dna was obtained, the n50 was 108,950 bp, and the overall length was 341,776,187 bp. the n50 of the transcriptome was 940 bp, […]

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PASA in publications

PMCID: 5941149
PMID: 29722814
DOI: 10.1093/gigascience/giy044

[…] genome using tophat2 [], which generated evidence of splice sites, introns, and exons. additionally, trinity (trinity, rrid:scr_013048), version 2.0.6, [], was utilized to assemble transcripts, and pasa (version 2.0.0) [] was used to group alternatively spliced isoforms. for the ab initio gene prediction, the standard augustus (version 3.0.3) pipeline was used to yield potentially predicted […]

PMCID: 5921998
PMID: 29703152
DOI: 10.1186/s12864-018-4701-2

[…] et (robertson and fish creek), and genemark es (goon nure). a training set based on est alignments (rna data sourced from the shintoku wgs project []) and transcoding regions was generated by pasa v2.1.0 [] and used to train all ab initio predictors except genemark es. alignment of est and protein evidence was performed with exonerate v2.2.0 [] using the coding2genome and protein2genome […]

PMCID: 5915607
PMID: 29691383
DOI: 10.1038/s41467-018-03423-5

[…] (fig. ) were assembled by trinity (version 2.0) . the trinity assembly included 183,515 contigs with an average length of 592 bp. these assembled sequences were aligned against the g. elata genome by pasa (program to assemble spliced alignment). valid transcript alignments were clustered based on genome mapping location and assembled into gene structures. gene models created by pasa were denoted a […]

PMCID: 5906906
PMID: 29635287
DOI: 10.1093/gigascience/giy038

[…] prediction, musk gland rna-seq data were assembled using trinity (trinity, rrid:scr_013048) with genome guide and de novo mode, respectively. the gene structures were obtained using pasa pipeline (version 2.0.2) []. we used evm (version 1.1.1) to integrate the above evidence and obtained a consensus gene set []. apollo (version 1.11.6) was performed to manually inspect gene […]

PMCID: 5870257
PMID: 29580224
DOI: 10.1186/s12864-018-4610-4

[…] by gsnap v.2014.7.21 [] to generate a bam file as the input. the resulting transcripts from these two modes were combined and aligned to the genome assembly with gmap v.2014.7.21 [] incorporated in program to assemble spliced alignments (pasa) pipeline v.2.0.2 [] to build a complete set of transcripts. homologs from predicted proteins of h. irregulare tc 32–1 available in mycocosm at joint […]

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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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