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  • Feedback on TFLOW: De Novo Transcriptome Assembly Pipeline

    Hi All!
    I've been working for a few months on a command-line de novo transcriptome assembly pipeline called TFLOW (Transcriptome-Flow). I wanted to see if anyone might be interested in using/testing it and giving me some feedback on whether it is useful!

    It can be downloaded here: http://www.github.com/fsugenomics/TFLOW/

    The TFLOW framework supports a few different assembly pipes at this point, and is designed to be modular so different pipe segments can be inserted.
    The main Trinity_Pipe is based on Trinity for primary sequence assembly but builds on Trinity by providing several auxiliary features. These include:
    - Read File Parsing (where applicable)
    - External Trimmomatic Read Trimming, for maximum flexibility of accessibility and reproducibility,
    - Trinity Assembly, with any desired parameters passed through,
    - CAP3 Assembly on Trinity output, prepares single-tissue assemblies for combination into a multi-organism/multi-tissue transcriptome.
    - Automatic Statistical Analysis on Trinity and CAP3 Outputs (Total, min-len, max-len, N50, etc…)
    - Automated analysis to determine the amount of genes from two benchmarking gene databases via BLAST Homology:
    - CEGMA (Core Eukaryotic Gene Database)
    - BUSCO (Further Benchmarking Genes that are Species-Subset Specific)

    To combine multiple tissues, a similar CAP3 Pipeline is used within the TFLOW Framework:
    - CAP3 (to combine individual tissue transcriptomes)
    - Statistical Analysis
    - CEGMA and BUSCO Gene Recapture Analyses

    The pipeline is designed to be easily-accessible while still allowing the full breadth of features for each of the component segments by allowing advanced parameter passthrough.

    The Trimmomatic read trimming parameters default to a minimum quality threshold of PHRED:30 for each read, Illumina adapter trimming, and a minimum length of 75bp, but all Trimmomatic, Trinity, and CAP3 settings can be easily changed as desired for a particular project.

    If you use different assembly or analysis steps in your transcriptome assembly process, I would be very interested in communicating to find out what they are! TFLOW has been designed to work with modular “segments,” so I would like to create and include modules that would work with whatever process is needed for a particular type of work.

    Please let me know what you think!

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