Metatranscriptomics is the analysis of the RNA transcripts being expressed by a community at a given point of time

Source text:
(Poretsky et al., 2005) Analysis of microbial gene transcripts in environmental samples. Appl Environ Microbiol.

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IMP
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IMP Integrated Meta-omic Pipeline

Is developed to perform large-scale, reproducible and automated integrative…

Is developed to perform large-scale, reproducible and automated integrative reference free analysis of metagenomic and metatranscriptomic data. IMP incorporates robust read preprocessing, iterative…

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SortMeRNA
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SortMeRNA

Software designed to rapidly filter ribosomal RNA fragments from…

Software designed to rapidly filter ribosomal RNA fragments from metatranscriptomic data produced by next-generation sequencers.

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d2-tools
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d2-tools

Toolbox for counting the frequency of K-tuple from sequencing datasets and…

Toolbox for counting the frequency of K-tuple from sequencing datasets and calculate the dissimilarity.

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riboPicker
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riboPicker

Automatically identify and efficiently remove rRNA-like sequences from…

Automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets.

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rRNAFilter
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rRNAFilter

Removes rRNA reads from metatranscriptomic datasets. rRNAFilter does not…

Removes rRNA reads from metatranscriptomic datasets. rRNAFilter does not require any prior knowledge of known rRNA sequences. It filters rRNA reads based on the difference of the frequency of k-mers…

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metaModules
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metaModules

A methodology for comparative metatranscriptomics that facilitates the…

A methodology for comparative metatranscriptomics that facilitates the automated identification of metabolic hotspots that are significantly deregulated in disease, and recovered disease-associated…

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TAG
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TAG

A reads mapping algorithm for mapping of short reads onto a de Bruijn graph of…

A reads mapping algorithm for mapping of short reads onto a de Bruijn graph of assemblies. A hash table of junction k-mers (k-mers spanning branching structures in the de Bruijn graph) is used to…

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SAMSA
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SAMSA Simple Analysis of Metatranscriptome Sequence Annotations

A bioinformatics pipeline designed to fully analyze and characterize activity…

A bioinformatics pipeline designed to fully analyze and characterize activity within a metatranscriptome, illustrating relative level of activity split by both organism and functional category. There…

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IDBA-MT
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IDBA-MT

An iterative De Bruijn Graph De Novo short read assembler for…

An iterative De Bruijn Graph De Novo short read assembler for meta-transcriptome.

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Anvi'o
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Anvi'o analysis and visualization platform for 'omics data

Brings together many aspects of today’s cutting-edge genomic, metagenomic,…

Brings together many aspects of today’s cutting-edge genomic, metagenomic, and metatranscriptomic analysis practices to address a wide array of needs. Anvi’o is an advanced analysis and…

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IDBA-MTP
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IDBA-MTP

Adopts a novel approach to metatranscriptomic assembly that makes use of the…

Adopts a novel approach to metatranscriptomic assembly that makes use of the fact that there is a database of millions of known protein sequences associated with mRNAs. How to effectively use the…

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GIST
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GIST Generative Inference of Sequence Taxonomy

A package containing a taxonomic classifier. GIST is focused specifically on…

A package containing a taxonomic classifier. GIST is focused specifically on the problem of annotating short (76 nucleotides and higher), unassembled reads with little or no quality filtering. It…

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rRNASelector
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rRNASelector

A computer program for selecting rRNA genes from metagenomic and…

A computer program for selecting rRNA genes from metagenomic and metatranscriptomic sequences.

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