Any good meta-transcriptomics pipelines

• sourmash

  1 432 9.4 Python

  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 ?

• biobakery_workflows

  1 92 6.7 Python

  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

• WorkOS

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• GEMAP_NCLDV

  1 3 10.0 Python

  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

Suggest a related project