ASaiM: an environment to analyze intestinal microbiota - Demo with analysis of gut metatranscriptomic sequences

ASaiM An intuitive and adjustable pipeline to process metatranscriptomic data from

intestinal microbiota

Bérénice Batut, Clémence Defois, Céline Ribière, Cyrielle Gasc, Jean-François Brugère, Eric Peyretaillade, CPER consortium Environnement

Digestif, Pierre Peyret

ASaiM An intuitive and adjustable pipeline to process metatranscriptomic data from

intestinal microbiota

Bérénice Batut, Clémence Defois, Céline Ribière, Cyrielle Gasc, Jean-François Brugère, Eric Peyretaillade, CPER consortium Environnement

Digestif, Pierre Peyret

ASaiM An environment to analyze

intestinal microbiota Demo with analysis of gut

metatranscriptomic sequences

Why ASaiM?

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Why ASaiM?

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Why ASaiM?

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Gut metagenomic projects

NCBI 2318

ENA 1103

DDBJ 28

MG-Rast 46

Camera 3

Total 3508

Why ASaiM?

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Gut metagenomic projects

NCBI 2318

ENA 1103

DDBJ 28

MG-Rast 46

Camera 3

Total 3508

But Difficult to query those databases Not standardized information

Why ASaiM?

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Available tools for metagenomic and metatranscriptomic sequence processing

Why ASaiM?

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Available tools for metagenomic and metatranscriptomic sequence processing

But

Almost nothing for metatranscriptomic sequences Difficult to use Not adjustable Only one step in sequence processing and analysis

A complete solution

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A complete solution

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ASaiM framework A solution to process sequences

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Philosophy Easy to use Adjustable

Demo on gut metatranscriptomic sequences

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Proposed sequence process pipeline

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Proposed sequence process pipeline

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Checkout the code!

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Download source code Move to demo directory

$ git clone https://github.com/ASaiM/ASaiM.git

$ cd demo

$ ls

config_file.json R2_sequences.fastq R1_sequences.fastq

config_file.json

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Download source code Move to demo directory

$ git clone https://github.com/ASaiM/ASaiM.git

$ cd demo

$ ls

config_file.json R2_sequences.fastq R1_sequences.fastq

Your pipeline = Your config_file.json

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Web interface

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h#p://g2im.u-‐clermont1.fr/asaim/

(Really) easy pipeline execution

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Install requirements Docker Docker-compose make

(Really) easy pipeline execution

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Install requirements Docker Docker-compose make

Execute the pipeline

$ cd demo/

$ make –f ../Makefile run_pipeline

What is behind the magic?

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What is behind the magic?

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Generated outputs

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2015-07-02_19-31/ report.txt quality_estimation/ FastQC/ quality_treatments/ Prinseq/ paired_end_assembly/ FastQ_Join/ rna_sorting/ SortMeRNA/ non_rRNA_taxonomic_assignation/ MetaPhlAn/ protein_ncrna_db_search/ search_against_cog/ Blast/

Generated outputs

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k__Bacteria 100.0 k__Bacteria|p__Bacteroidetes 95.68413 k__Bacteria|p__Fusobacteria 4.31587 k__Bacteria|p__Bacteroidetes|c__Bacteroidia 92.62004 k__Bacteria|p__Fusobacteria|c__Fusobacteria 4.31587 k__Bacteria|p__Bacteroidetes|c__Flavobacteria 3.06409 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales 92.62004 k__Bacteria|p__Fusobacteria|c__Fusobacteria|o__Leptotrichales 4.31587 k__Bacteria|p__Bacteroidetes|c__Flavobacteria|o__Flavobacteriales 3.06409 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae 88.87376 k__Bacteria|p__Fusobacteria|c__Fusobacteria|o__Leptotrichales|f__Leptotrichales_unclassified 4.31587 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae 3.74628 k__Bacteria|p__Bacteroidetes|c__Flavobacteria|o__Flavobacteriales|f__Flavobacteriaceae 3.06409 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides 88.87376 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Parabacteroides 3.74628 k__Bacteria|p__Bacteroidetes|c__Flavobacteria|o__Flavobacteriales|f__Flavobacteriaceae|g__Cellulophaga 3.06409 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_unclassified 88.87376 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Parabacteroides|s__Parabacteroides_unclassified 3.74628 k__Bacteria|p__Bacteroidetes|c__Flavobacteria|o__Flavobacteriales|f__Flavobacteriaceae|g__Cellulophaga|s__Cellulophaga_unclassified

3.06409

report.txt Executed treatments and some results

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Pretreatments... Quality control... Quality esOmaOon... Run FastQC... Quality treatment... Run PRINSEQ... 60 bad sequences for R1 979 bad sequences for R2 6136 conserved sequences for R1 5217 conserved sequences for R2 Paired-‐end assembly... Run FastQ_Join... 3777 joined sequences 2359 single sequences for R1 1440 single sequences for R2 RNA sorOng... Run SortMeRNA... 1465 rRNA sequences 2312 non rRNA sequences

Taxonomic assignaOon... Non rRNA sequence taxonomic assignaOon... Run MetaPhlAn…

FuncOonal assignaOon... Search against protein and ncRNA databases... Search against COG database... Run Blast…

Current status

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Core structure Available

7 tools 1 sequence database (COG)

Open-source Documentation

https://asaim.github.io/

ASaiM

What’s next?

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Short term More detailed reports Addition of visualization tools Tests

Long term

More tools and treatments Better web interface Expert database

Who is involved?

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CPER consortium Environnement digestif

Want to try? We need feedback!!

Tools and treatments to add? Ideas?

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http://asaim.github.io/

Science

ASaiM: an environment to analyze intestinal microbiota - Demo with analysis of gut metatranscriptomic sequences