Any good meta-transcriptomics pipelines

This page summarizes the projects mentioned and recommended in the original post on /r/bioinformatics

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  1. sourmash

    Quickly search, compare, and analyze genomic and metagenomic data sets.

    have you seen https://www.nature.com/articles/s41587-019-0209-9?ref=https://githubhelp.com and https://github.com/sourmash-bio/sourmash ?

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  3. biobakery_workflows

    bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.

    The bio bakery has some meta-transcriptomic pipelines on it. They also maintain the mertaphlan and humann packages that are almost becoming the defacto standard when analysing shot gun reads. https://github.com/biobakery/biobakery_workflows

  4. GEMAP_NCLDV

    Genome Mapping Analysis Pipeline for giant viruses

    I developed a pipeline for doing metatranscriptomics with time series data. Check it out here https://github.com/BenMinch/GEMAP_NCLDV

NOTE: The number of mentions on this list indicates mentions on common posts plus user suggested alternatives. Hence, a higher number means a more popular project.

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