PMID- 28451381
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20240326
IS  - 2046-1402 (Print)
IS  - 2046-1402 (Electronic)
IS  - 2046-1402 (Linking)
VI  - 4
DP  - 2015
TI  - MetaGenSense: A web-application for analysis and exploration of high throughput 
      sequencing metagenomic data.
PG  - 86
LID - 10.12688/f1000research.6139.3 [doi]
LID - 86
AB  - The detection and characterization of emerging infectious agents has been a 
      continuing public health concern. High Throughput Sequencing (HTS) or 
      Next-Generation Sequencing (NGS) technologies have proven to be promising 
      approaches for efficient and unbiased detection of pathogens in complex 
      biological samples, providing access to comprehensive analyses. As NGS approaches 
      typically yield millions of putatively representative reads per sample, efficient 
      data management and visualization resources have become mandatory. Most usually, 
      those resources are implemented through a dedicated Laboratory Information 
      Management System (LIMS), solely to provide perspective regarding the available 
      information. We developed an easily deployable web-interface, facilitating 
      management and bioinformatics analysis of metagenomics data-samples. It was 
      engineered to run associated and dedicated Galaxy workflows for the detection and 
      eventually classification of pathogens. The web application allows easy 
      interaction with existing Galaxy metagenomic workflows, facilitates the 
      organization, exploration and aggregation of the most relevant sample-specific 
      sequences among millions of genomic sequences, allowing them to determine their 
      relative abundance, and associate them to the most closely related organism or 
      pathogen. The user-friendly Django-Based interface, associates the users' input 
      data and its metadata through a bio-IT provided set of resources (a Galaxy 
      instance, and both sufficient storage and grid computing power). Galaxy is used 
      to handle and analyze the user's input data from loading, indexing, mapping, 
      assembly and DB-searches. Interaction between our application and Galaxy is 
      ensured by the BioBlend library, which gives API-based access to Galaxy's main 
      features. Metadata about samples, runs, as well as the workflow results are 
      stored in the LIMS. For metagenomic classification and exploration purposes, we 
      show, as a proof of concept, that integration of intuitive exploratory tools, 
      like Krona for representation of taxonomic classification, can be achieved very 
      easily. In the trend of Galaxy, the interface enables the sharing of scientific 
      results to fellow team members.
FAU - Correia, Damien
AU  - Correia D
AD  - Pole Genotypage des Pathogenes, Unite Environnement et Risques Infectieux, 
      Institut Pasteur, F-75724, Paris, France.
FAU - Doppelt-Azeroual, Olivia
AU  - Doppelt-Azeroual O
AD  - Centre de Bioinformatique, Biostatistique et Biologie Integrative (C3BI, USR 3756 
      Institut Pasteur et CNRS), Institut Pasteur, F-75724, Paris, France.
FAU - Denis, Jean-Baptiste
AU  - Denis JB
AD  - Groupe Exploitation et Infrastructure, Institut Pasteur, F-75724, Paris, France.
FAU - Vandenbogaert, Mathias
AU  - Vandenbogaert M
AD  - Pole Genotypage des Pathogenes, Unite Environnement et Risques Infectieux, 
      Institut Pasteur, F-75724, Paris, France.
FAU - Caro, Valerie
AU  - Caro V
AD  - Pole Genotypage des Pathogenes, Unite Environnement et Risques Infectieux, 
      Institut Pasteur, F-75724, Paris, France.
LA  - eng
PT  - Journal Article
DEP - 20150402
PL  - England
TA  - F1000Res
JT  - F1000Research
JID - 101594320
PMC - PMC5405795
OTO - NOTNLM
OT  - Django
OT  - Galaxy
OT  - High Throughput Sequencing
OT  - Laboratory Information Management System
OT  - Next-Generation Sequencing
COIS- Competing interests: No competing interests were disclosed.
EDAT- 2015/04/02 00:00
MHDA- 2015/04/02 00:01
PMCR- 2016/12/01
CRDT- 2017/05/02 06:00
PHST- 2016/11/25 00:00 [accepted]
PHST- 2017/05/02 06:00 [entrez]
PHST- 2015/04/02 00:00 [pubmed]
PHST- 2015/04/02 00:01 [medline]
PHST- 2016/12/01 00:00 [pmc-release]
AID - 10.12688/f1000research.6139.3 [doi]
PST - epublish
SO  - F1000Res. 2015 Apr 2;4:86. doi: 10.12688/f1000research.6139.3. eCollection 2015.