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ASaiM
An intuitive and adjustable pipeline to
process metatranscriptomic data from
intestinal microbiota
Bérénice Batut,
C...
ASaiM
An intuitive and adjustable pipeline to
process metatranscriptomic data from
intestinal microbiota
Bérénice Batut,
C...
Why ASaiM?
3



 
Why ASaiM?
4


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 

 

 
...
Why ASaiM?
5
Gut metagenomic projects
NCBI 2318
ENA 1103
DDBJ 28
MG-Rast 46
Camera 3
Total 3508
Why ASaiM?
6
Gut metagenomic projects
NCBI 2318
ENA 1103
DDBJ 28
MG-Rast 46
Camera 3
Total 3508
But
Difficult to query those...
Why ASaiM?
7
Available tools for metagenomic and
metatranscriptomic sequence processing
Why ASaiM?
8
Available tools for metagenomic and
metatranscriptomic sequence processing
But
Almost nothing for metatranscr...
A complete solution
9





...
A complete solution
10
ASaiM framework
A solution to process sequences
11

 




...
ASaiM framework
A solution to process sequences
12

 




...
ASaiM framework
A solution to process sequences
13
Philosophy
Easy to use
Adjustable

 
...
Demo on gut
metatranscriptomic sequences
14




...
Proposed sequence process pipeline
15
Proposed sequence process pipeline
16
Checkout the code!
17
Download source code
Move to demo directory
$ git clone https://github.com/ASaiM/ASaiM.git	
$ cd dem...
config_file.json
18
Download source code
Move to demo directory
$ git clone https://github.com/ASaiM/ASaiM.git	
$ cd demo	
$...
Your pipeline = Your config_file.json
19
 



...
Your pipeline = Your config_file.json
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 



...
Your pipeline = Your config_file.json
21
 

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
...
Your pipeline = Your config_file.json
22
 

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
...
Web interface
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h#p://g2im.u-­‐clermont1.fr/asaim/	
  
(Really) easy pipeline execution
24
Install requirements
Docker
Docker-compose
make
(Really) easy pipeline execution
25
Install requirements
Docker
Docker-compose
make
Execute the pipeline
$ cd demo/	
$ mak...
What is behind the magic?
26
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



 
...
What is behind the magic?
27





 
...
Generated outputs
28
2015-07-02_19-31/	
	
report.txt	
	
quality_estimation/	
	
 	
FastQC/	
	
quality_treatments/	
	
 	
Pri...
Generated outputs
29
2015-07-02_19-31/	
	
report.txt	
	
quality_estimation/	
	
 	
FastQC/	
	
quality_treatments/	
	
 	
Pri...
report.txt
Executed treatments and some results
30
2015-07-02_19-31/	
	
report.txt	
	
quality_estimation/	
	
 	
FastQC/	
	...
Current status
31
Core structure
Available
7 tools
1 sequence database (COG)
Open-source
Documentation
https://asaim.githu...
What’s next?
32
Short term
More detailed reports
Addition of visualization tools
Tests
Long term
More tools and treatments...
Who is involved?
33


CPER consortium Environnement digestif
Want to try?
We need feedback!!
Tools and treatments to add?
Ideas?
34
http://asaim.github.io/
Prochain SlideShare
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JOBIM 2015 - ASaiM: an environment to analyze intestinal microbiota - Demo with analysis of gut metatranscriptomic sequences

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More information about the project are available at http://asaim.github.io/

Metatranscriptomic data allow active microbial communities description by gene products analysis. In comparison to metagenomic studies, few metatranscriptomic data have been obtained on environmental ecosystems (soil, water, mine drainage…) as on human-associated microbiota despite health concerns. This discrepancy is due to difficulties in RNA recovery but also to a lack of tools dedicated to metatranscriptomic data processing. Nevertheless, some homemade pipelines adapted from metagenomics analyses exist but are not freely available and thus not easily accessible. Here we present ASAIM (Auvergne Sequence Analysis for Intestinal Microbiota), a pipeline to process metatranscriptomic data from intestinal microbiota. Starting from raw reads, it generates taxonomic and functional assignments using databases dedicated to this microbiome. These gut databases become more and more supplied by large metagenomic projects (like MetaHIT and HMP projects for microbial reference genomes) and therefore useful for reliable and accurate assignments. Finally, ASAIM combines taxonomic, functional and abundance information, coupled to statistical analyses and data mining tools. This pipeline is designed to be adjustable (personalized or proposed data processing given the type of data) and intuitive with its web interface, documentation and tutorials. ASAIM is freely available at http://g2im.u-clermont1.fr/asaim/ and can be downloaded or directly interrogated through its web interface.

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JOBIM 2015 - ASaiM: an environment to analyze intestinal microbiota - Demo with analysis of gut metatranscriptomic sequences

  1. 1. 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
  2. 2. 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  
  3. 3. Why ASaiM? 3     
  4. 4. Why ASaiM? 4                 
  5. 5. Why ASaiM? 5 Gut metagenomic projects NCBI 2318 ENA 1103 DDBJ 28 MG-Rast 46 Camera 3 Total 3508
  6. 6. Why ASaiM? 6 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
  7. 7. Why ASaiM? 7 Available tools for metagenomic and metatranscriptomic sequence processing
  8. 8. Why ASaiM? 8 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
  9. 9. A complete solution 9       
  10. 10. A complete solution 10
  11. 11. ASaiM framework A solution to process sequences 11          
  12. 12. ASaiM framework A solution to process sequences 12                 
  13. 13. ASaiM framework A solution to process sequences 13 Philosophy Easy to use Adjustable                 
  14. 14. Demo on gut metatranscriptomic sequences 14           
  15. 15. Proposed sequence process pipeline 15
  16. 16. Proposed sequence process pipeline 16
  17. 17. Checkout the code! 17 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
  18. 18. config_file.json 18 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                                                                
  19. 19. Your pipeline = Your config_file.json 19                          
  20. 20. Your pipeline = Your config_file.json 20                                                             
  21. 21. Your pipeline = Your config_file.json 21                                     
  22. 22. Your pipeline = Your config_file.json 22                                           
  23. 23. Web interface 23 h#p://g2im.u-­‐clermont1.fr/asaim/  
  24. 24. (Really) easy pipeline execution 24 Install requirements Docker Docker-compose make
  25. 25. (Really) easy pipeline execution 25 Install requirements Docker Docker-compose make Execute the pipeline $ cd demo/ $ make –f ../Makefile run_pipeline
  26. 26. What is behind the magic? 26                  
  27. 27. What is behind the magic? 27                  
  28. 28. Generated outputs 28 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/
  29. 29. Generated outputs 29 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/ 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  
  30. 30. report.txt Executed treatments and some results 30 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/ 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…  
  31. 31. Current status 31 Core structure Available 7 tools 1 sequence database (COG) Open-source Documentation https://asaim.github.io/ ASaiM
  32. 32. What’s next? 32 Short term More detailed reports Addition of visualization tools Tests Long term More tools and treatments Better web interface Expert database
  33. 33. Who is involved? 33   CPER consortium Environnement digestif
  34. 34. Want to try? We need feedback!! Tools and treatments to add? Ideas? 34 http://asaim.github.io/

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