Metatranscriptomics Workflow Questions?

This page summarizes the projects mentioned and recommended in the original post on /r/bioinformatics
Genomics cog-assignment metagenomics Annotation uniprot

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  • MOSCA

    Meta-Omics Software for Community Analysis (by iquasere)

    • I have developed a pipeline (https://github.com/iquasere/MOSCA) that performs integrated MG and MT analysis, using similar steps to those you have listed. If you provide it only MT, it will assemble the MT using Trinity (MEGAHIT was developed for MG analysis), but it is preferable that you use a reference metagenomics dataset (you can also input it that), so you obtain better contigs, better genes and a better reference for your MT. All this is obtained with MOSCA.

  • UPIMAPI

    UniProt Id Mapping through API

    • Prediction of coding sequences takes as input the contigs you obtained, and gives you the translated genes. Besides annotating with the KEGG database, you may also want to annotate with more general purpose databases (e.g. UniProt), as these provide more taxonomies and functional information. MOSCA includes UPIMAPI (https://github.com/iquasere/UPIMAPI) and reCOGnizer (https://github.com/iquasere/reCOGnizer), which annotate genes with reference to UniProt and CDD databases using two different methods, providing complementary information. This is the same methodology used by widely popular tools such as eggNOG-mapper and Prokka, but these use other databases.

  • InfluxDB

    Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

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  • reCOGnizer

    A tool for domain based annotation with databases from the Conserved Domains Database

    • Prediction of coding sequences takes as input the contigs you obtained, and gives you the translated genes. Besides annotating with the KEGG database, you may also want to annotate with more general purpose databases (e.g. UniProt), as these provide more taxonomies and functional information. MOSCA includes UPIMAPI (https://github.com/iquasere/UPIMAPI) and reCOGnizer (https://github.com/iquasere/reCOGnizer), which annotate genes with reference to UniProt and CDD databases using two different methods, providing complementary information. This is the same methodology used by widely popular tools such as eggNOG-mapper and Prokka, but these use other databases.

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