Downloads

Pathseq2.0 : version 1.0 - HPC version

  • Click here to obtain the latest release of Pathseq pipeline.

    Update:
    Run PathSeq on the HPC cluster
    Please contact us, if you have questions

  • Click here to obtain sample input file to run PathSeq pipeline.

    Database files are below (Version: Oct 2015)
  • README
  • Click here to obtain Bacteria Database Fasta file.
  • Click here to obtain Fungi Database Fasta file.
  • Click here to obtain Virus Database Fasta file.
  • Click here to obtain Archaea Database Fasta file.
  • Click here to obtain Virus Database Fasta file.
  • Click here to obtain Phage Database Fasta file.
  • Click here to obtain Human plus Microbial Database Fasta file.
  • Click here to obtain Human Ensembl_plus_RNA Database Fasta file.
  • Click here to obtain Female reference Database Fasta file.
  • Click here to obtain Human Genome_plus_Transcriptome Database Fasta file.
  • Click here to obtain Human reference genome Database Fasta file.
Pathseq latest version: version 1.5 (updated May, 2014) - Cloud Version
  • Click here to obtain the latest release of Pathseq pipeline.

    Update:
    Minor bugs are fixed
    Blastn in the Postsubtraction..mapping to microbial database+human database is replaced with Megablast
    Please contact us, if you have questions

  • Click here to obtain sample input file to run PathSeq pipeline.
Pathseq latest version: version 1.4 (updated Apr, 2014) - Cloud Version
  • Click here to obtain the latest release of Pathseq pipeline.

    Update:
    S3CMD command linehas been updated
    Please contact us, if you have questions

  • Click here to obtain sample input file to run PathSeq pipeline.
  • Click here to Installation manual.
  • Click here to User Manual.
Pathseq latest version: version 1.3 (updated Feb, 2014) - Cloud Version
  • Click here to obtain the latest release of Pathseq pipeline.

    Update:
    S3CMD has been updated
    Please contact us, if you have questions

  • Click here to obtain sample input file to run PathSeq pipeline.
Pathseq latest version: version 1.2 (updated Agust, 2012) - Cloud version
  • Click here to obtain the latest release of Pathseq pipeline.

    Update: BWA aligner replaces the MAQ aligner
    S3CMD has been updated
    Added new datatype called DATATYPE (WGS/RNASEQ). This helps the pipeline to select the databases (reference genomes)
    Hadoop framework has been updated to 1.0.3
    Please contact us, if you have questions

  • Click here to obtain sample input file to run PathSeq pipeline.
Pathseq latest version: (updated July 28, 2011) - Cloud version
  • Click here to obtain the latest release of Pathseq pipeline.

    Update: Base AMI has been replaced with new base AMI.
    Note: This won't effect the users who already created their own AMI's using create_ownAMI.com script with the package.
    Please contact us, if you have questions

  • Click here to obtain sample input file to run PathSeq pipeline.
Pathseq old versions:
  • Click here to obtain the latest release of Pathseq pipeline.












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