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David Rissato Cruz edited this page Jun 10, 2019
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Welcome to the idseq-dag wiki!
IDseq is a hypothesis-free global software platform that helps scientists identify pathogens in metagenomic sequencing data.
- Discover - Identify the pathogen landscape
- Detect - Monitor and review potential outbreaks
- Decipher - Find potential infecting organisms in large datasets
A collaborative open project of Chan Zuckerberg Initiative and Chan Zuckerberg Biohub. Check out our repositories:
- idseq-web - Frontend portal (here)
- idseq-dag - Bioinformatics pipeline and workflow engine
- idseq-cli - Command line upload interface
- idseq-bench - Pipeline benchmarking tools
The documentation presented here reflects the current IDseq pipeline status and processes, with descriptions of the parameters used. It is divided into three main analysis sections.
- Host Filtering and QC
- Alignment and Taxonomic Aggregation
- Reporting and Visualization
The pipeline relies on a variety of different softwares, whose versions are listed below. The most up-to-date version information can be found in the dockerfile
| Dependency | Version |
|---|---|
| Python | 3.6 |
| STAR | 2.5.3a |
| Trimmomatic | 0.38 |
| PriceSeqFilter | source |
| cd-hit-dup | 4.6.8 |
| HTSeq | 0.6.1 |
| Bowtie2 | 2.3.2 |
| Gsnap | source 2017-11-15 |
| Samtools | 1.5 |
| Spades | 3.11.0 |
| ncbi-blast | 2.6.0 |
| kSNP3.1 | source |
| SRST2 | Python3 Compatible Fork |