Web Service BioMaS REST It

aka Bioinformatic analysis of Metagenomic AmpliconS Add_annotation_inactiveAdd_annotation_inactiveLog in to add alternative_name
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Overview

Provider:
Icon  INFN Bari

Location:
Italy It

Submitter/Source:
Pasquale NotarangeloIt (over 3 years ago)

Base URL:
http://webgateway.ba.infn.it:8080/INFN.Grid.FrontEnd

Description(s):
by Bruno Fosso (over 3 years ago)

BioMaS

BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data arrangement to final taxonomic identification, that are absolutely required in a typical Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the output of the Illumina platforms.

Description

The BioMaS workflow allows the analysis of Illumina read datasets and includes the following consecutively and automatically running modules:

  • 1. The first module starts with the raw data evaluation and arrangement for the next analysis step. Namely, the FastQC [1] tool executes a statistical and quality snapshot of the reads. Subsequently, the tool Flash [2] merges the overlapping paired-end reads and the obtained longer sequences are dereplicated using Usearch [3]. The not overlapping read pairs are analysed separately in order to trim low quality regions and to remove pairs containing less than 50 nt long reads;
  • 2. All the rearranged sequences are mapped on meta-barcodes reference databases, namely RDP II [4] and ITSoneDB [5], implemented in the system, by means of Bowtie2 and the resulting data are stored in a bam file. Then, for each query sequence (or pairs), the mapping hits are parsed, according to several parameters (such as identity percentage and query coverage) and the most significant ones are annotated in a match file;
  • 3. In the final module the match file is processed by TANGO [6] in order to map the sequences on the reference NCBI taxonomy. As a result, BioMaS produces a graphical three and several pie-charts describing the taxonomic complexity of the investigated microbiota at different rank (from phylum to species). All the BioMaS components have been developed by using Python and Bash scripts integrating third-party tools.

Job submission

The job submission requires to enter the following objects:

  • R1: R1 reads file produced by Illumina platform software;
  • R2: R2 reads file produced by Illumina platform software;
  • Database: the database (RDP II or ITSoneDB) used for the comparison;
  • Base name: a prefix name, defined by the user, for the output data;
  • Recipient email address: email address to which the final results should be sent. The R1 and the R2 files are produced by Illumina platform for each sample in fastq format as compressed “gzip” file. BioMaS is able to directly process both the fastq or the gz files.

Job retrieval

An e-mail with an HTML report including the produced graphical results of taxonomic inference performed by BioMaS and the statistical and qualitative evaluation of the initial reads dataset performed with FastQC will be sent to the address previously registered by the user.

Reference

  • 1.FastQC Available from: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
  • 2.Magoc, T. and S.L. Salzberg, FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics, 2011. 27(21): p. 2957-63.
  • 3.Edgar, R.C., Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 2010. 26(19): p. 2460-1.
  • 4.Cole, J.R., et al., The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res, 2009. 37(Database issue): p. D141-5.
  • 5.Santamaria, M., et al., Reference databases for taxonomic assignment in metagenomics. Brief Bioinform, 2012. 13(6): p. 682-95.
  • 6.Alonso-Alemany, D., et al., Further Steps in TANGO: improved taxonomic assignment in metagenomics. Bioinformatics, 2014. 30(1): p. 17-23.
ELIXIR Description(s): Info
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License(s): Info
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Cost: Info
by Bruno Fosso (almost 3 years ago)

Free

Usage conditions: Info
by Bruno Fosso (almost 3 years ago)

3 requests per day

Contact info: Info
by Bruno Fosso (over 3 years ago)

Prof. Graziano Pesole: g.pesole@ibbe.cnr.it Dr. Bruno Fosso: b.fosso@ibbe.cnr.it Dr. Monica Santamaria: m.santamaria@ibbe.cnr.it

How to cite this service: Info
by Bruno Fosso (over 1 year ago)

Fosso B, Santamaria M, Marzano M, Alonso-Alemany D, Valiente G, Donvito G, Monaco A, Notarangelo P, Pesole G: BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS. BMC bioinformatics 2015, 16:203.

Publications about this service: Info
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Citations of this service: Info
by Bruno Fosso (almost 3 years ago)

@article{Manzari2014, author = {Manzari, Caterina and Fosso, Bruno and Marzano, Marinella and Annese, Anita and Caprioli, Rosa and D’Erchia, Anna Maria and Gissi, Carmela and Intranuovo, Marianna and Picardi, Ernesto and Santamaria, Monica and Scorrano, Simonetta and Sgaramella, Giuseppe and Stabili, Loredana and Piraino, Stefano and Pesole, Graziano}, doi = {10.1007/s10530-014-0810-2}, file = , issn = {1387-3547}, journal = {Biological Invasions}, month = nov, title = {{The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy}}, url = {http://link.springer.com/10.1007/s10530-014-0810-2}, year = {2014} }

Example workflows using this service: Info
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Maturity level of this service (from the BioVeL wiki) and actions to improve it: Info
by Aleksandra Nenadic Admin(about 3 hours ago)
https://wiki.biovel.eu/display/doc/BioVeL+Service+-+BioMaS

Actions to improve the service description

Provisional maturity level: 0

To obtain level 1, this service requires the following 1 actions:

- Add documentation link

by Bruno Fosso (about 3 hours ago)
https://wiki.biovel.eu/display/doc/BioVeL+Service+-+BioMaS

Actions to improve the service description

Provisional maturity level: 0

To obtain level 1, this service requires the following 1 actions:

- Add documentation link