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GATK PathSeq (released January 2018)

  • The latest version of PathSeq is available as a part of the Genome Analysis Toolkit (GATK), which can be downloaded from github.
  • Pre-built host and microbe reference files are available in the GATK Resource Bundle on the FTP server under /bundle/beta/PathSeq.

Old Versions of PathSeq **DEPRECATED**

Pathseq2.0 : HPC release

  • Click here to obtain this release.
  • Click here to obtain sample input file.

    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 version 1.5 (updated May, 2014) - Cloud Version
  • Update: minor bugs are fixed, Blastn in the postsubtraction, mapping to microbial database+human database is replaced with Megablast
  • Click here to obtain this release.
  • Click here to obtain sample input file to run PathSeq pipeline.
Pathseq latest version: version 1.4 (updated Apr, 2014) - Cloud Version
  • Update: S3CMD command linehas been updated
  • Click here to obtain the latest release of Pathseq pipeline.

  • 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 Pathseq version 1.2 (updated August, 2012) - Cloud version
  • 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.
  • Click here to obtain the latest release of Pathseq pipeline.
  • Click here to obtain sample input file to run PathSeq pipeline.
Pathseq update (July 28, 2011) - Cloud version
  • 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.
  • Click here to obtain this release.
  • Click here to obtain sample input file.
Pathseq old versions:










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