Anvaya : A Workflow Environment for High Throughput Comparative Genomics

Comprehensive analysis of heterogeneous genomic data requires a flexible platform for running complex queries that is capable of integrating and analyzing large amount of genomic data in pipeline. Anvaya is a software application consisting of interface to Bioinformatics tools and databases in a workflow environment, to execute the set of analyses tools in series or in parallel. One of the unique features of Anvaya is the rules engine that defines rules for logical connection between the existing tools. Anvaya offers the user, novel functionalities to carry out exhaustive comparative analysis via custom tools which are tools with new functionality not available in standard tools and built-in PERL parsers.It also provides a set of 13 pre-defined workflows for frequently used pipelines in genome annotation and comparative genomics ranging from EST assembly and annotation to phylogenetic reconstruction and analysis of next generation sequencing-NGS data (both genome as well as transcriptome)

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To Cite Anvaya

Paper Name:
- ANVAYA: A Workflows Environment For Automated Genome Analysis
Journal Name:
- Journal of Bioinformatics and Computational Biology (2012), DOI No: 10.1142/S0219720012410065
Author:
- Bhakti Limaye, Ruma Banerjee, Avik Datta, Harshal Inamdar, Pankaj Vats, Sonal Dahale, Alok Bhandari, E. P. Ramakrishnan, Rajnikanth Tupakula, Sandeep Malviya, Avinash Bayaskar, Renu Gadhari, Sankalp Jain, Vivek Gavane, Rashmi Mahajan, Sunitha K, AND Rajendra Joshi

Related Publication

Paper Name:
- Comparative genomics of cell envelope components in Mycobacterium
Journal Name:
- PloSOne (2011) 10.1371/journal.pone.0019280
Author:
- Ruma Banerjee, Pankaj Vats, Sonal Dahale, Sunitha Manjari Kasibhatla and Rajendra Joshi

Anvaya Tutorials

PDF Tutorials
EST assembly and annotation
Genome Annotation

Supporting Files

AraThiChr5_Subset.seq

PDF
Functional annotation

Supporting Files

FA_HandOutsProtein.seq

PDF
Prediction of orthologs
Prediction of remote orthologs

Supporting Files

remote.fasta

PDF
Prediction of motifs

Supporting Files

ara_test

PDF
Molecular Phylogenetic Reconstruction

Supporting Files

phylogeny.seq

PDF
Prediction of Primers

Supporting Files

maize_est_primer

PDF
Prediction of Promoters from Microarray data

Supporting Files

PDF
Prediction of Antigenic sites

Supporting Files

PDF
Differential Gene Expression Using RNA Seq

Supporting Files

PDF
Reference Mapping

Supporting Files

Sample Date Set Zip File

PDF

Anvaya Presentation

Anvaya Features

Anvaya User Registration

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Anvaya Distribution

  • Free Download Client Installer (Click here to download the Anvaya Client Installer Version 1.4)
    • Now with NGS support
    • Client can execute on Windows or Linux
    • Java 1.6+ must be pre-installed
  • Installation Instructions
    • To install AnvayaClient, the binay of Java i.e. java must be set in the Path variable. To verify just type "java -version" to get version information of java
    • Use the AnvayaInstaller to install Anvaya client on your machine. For Windows installation, double click the installer and follow further steps. For Linux installation, execute the installer using 'jar' command and follow further steps. java -jar AnvayaInstallerVx.y.z.jar
  • Usage
    • The client will interact with pre-installed server on C-DAC's BRAF facility (In the downloaded client, ensure Server and Proxy settings are properly done)
    • Kindly Register for dedicated login account. For trial purpose use guest account (login: guest, password: gue2Anv)
    • Login account will be valid for 6 months duration by default and may be extended on further request
    • Contact braf-help@cdac.in for any queries.
  • Standard Database integrated in Anvaya
    • Non-redundant protein database (nr)
    • UniProt Knowledgebase (UniProtKB)
    • Mitochondrial protein database (mito.aa)
    • Mitochondrial nucleotide database (mito.nt)
    • PDB protein database (pdbaa)
    • PDB nucleotide datase (pdbnt)
    • Vector database