Partek Flow
Description
Partek Flow (Partek) is a graphical user interface (GUI) based bioinformatics software that is dedicated to the analysis of next generation sequencing (NGS) data. It can perform the analyses listed below.
List of Analysis Functions
DNA sequencing
- Variant detection
- Germline
- Somatic
- Copy number
- Low frequency
- Causal
Gene expression
- RNA sequencing
- MicroRNA sequencing
- Single cell RNA sequencing
- CITE sequencing
- Microarray
Epigenetics
- ChIP sequencing
- ATAC sequencing
Microbial
- Metagenomics
Biological insights
- Pathway analysis
- Gene set enrichment analysis
Visualizations
- Genome browser
Recommendations
Partek Flow allows users to start a multiple stages of the analyses. For gene expression analysis by RNA sequencing, users can start an analysis using either raw sequencing reads (FASTQ), aligned reads (BAM), or count table. Partek Flow is developed by the company that makes Partek Genomics Suite, thus users can go offline and run some analyses in Partek Genomics Suite. The flexibility of being able to start at multiple stages of an analysis workflow and the ability to conduct analyses offline through Partek Genomics Suite are rationale for using this package.
Things to Know
Partek Flow runs on Biowulf (NIH high performance compute cluster), thus when using this package, users will not be limited by local compute resources. Users interface with this package via a web browser, so users will not have to install additional software.
Input Data Types
Partek Flow supports a range of data formats, thus allowing users the ability to enter an analysis pipeline at any stage. Below are the supported data formats.
- FASTQ
- FASTA
- BAM
- SAM
- VCF
- BCF
- TXT
- BGX
- MTX
- H5
- SRA
- SFF
- GZ
- TAR
- ZIP
- BPM
- CEL
- QUAL
- IDAT
- PROBE_TAB
Output Data Types
Graphical output can be exported as PNG or SVG images at a specified resolution. Tabular data as well as files generated during NGS analysis (i.e., BAM files) can be found in the corresponding project folder.
Access Information
To access Partek Flow, users need to first set up a Biowulf account by clicking here. Next, users will need to ensure they have enough space on Biowulf to store data. (Fill out the storage request form) if you need additional space. Finally, send an email to staff@hpc.nih.gov to get your Partek Flow account activated. When these steps are complete, go to https://partekflow.cit.nih.gov/flow to start using Partek Flow. Partek Flow users need to either be on the NIH network or connected via VPN. OSTR holds 5 Partek Flow and 3 Partek Flow single cell licenses.
Getting Help
Partek Flow comes with extensive documentation. BTEP also hosts Partek Flow training frequently.