NGS RESEQUENCING BROWSER

Introduction

With the advances in next generation sequencing (NGS) technology and significant reduction in sequencing costs it is now possible to sequence large sets of crop germplasm and generate whole genome scale structural variations and genotypic data. In depth informatics analysis of the genotypic data can provide better understanding of the links with the observed phenotypic changes. This approach can be used to further understand and study different traits for the improvement of crops by design.

Bioinformatics Analysis Pipeline

We have built a bioinformatics analysis pipeline for identification of SNPs and insertion, deletions using GATK3.0 software against soybean reference genome Gmax_275_Wm82.a2.v1. Downstream analysis is conducted for copy number variations (CNV) using CnMOPs and SNP annotations generated using SnpEff and SnpSift. Data is also analyzed using LDexplorer and in-house built tool SNPViz.



Analysis is conducted using XSEDE as the computing infrastructure, iPlant as the data and cloud infrastructure, and the Pegasus workflow systems to control and coordinate the data management and computational tasks. Each workflow gets mapped into three pegasus-mpi-cluster jobs; one with BWA going to the normal compute nodes, one for large memory Picard and GATK tasks mapped to the large memory nodes available on Stampede, and the last one lower memory GATK tasks. It outlines best practices for efficient utilization of distinct and unique Cyberinfrastructure (CI) resources available through multiple providers, with emphasis on creating extensible and scalable workflows that can be easily modified and deployed.



Data Generation Phases

We have generated resequencing data for several soybean lines from various projects using Illumina paired end sequencing technology. Details of soybean lines and traits selected are as follows:

Phase I: MSMC (15X)

  • Resequencing of 108 soybean germplasm lines from Dr. Nguyen lab (15X).
  • Soybean lines are selected for major traits including oil, protein, soybean cyst nematode resistance (SCN), abiotic stress resistance (drought, heat and salt) and root system architecture.
  • Sequencing done at BGI.

  • Phase II: USB (40X & 15X)

  • Resequencing of 350 soybean lines with industry partners (50 at 40X; 300 at 15X ).
  • Academic (MU) and Industry Partnership with Dow, Monsanto & Bayer.
  • Sequencing done at BGI.

  • USB (15X) (planned in future)

  • Resequencing of 500+ soybean lines.

  • Data Access

    Data is stored on iPlant Data Store cloud computing resources with controlled access. Data is available for access at multiple tiers including:

  • Raw reads (Fastq)
  • Alignments (BAM)
  • SNP & Indel (VCF, matrix)
  • SnpEff, CnMOPs results
  • Summary Files

  • * Note: This tool loads results files directly from iPlant data store. Some files may be temporarily inaccessible during the time of iPlant maintenance. Please re-access the link after the maintenance is complete or contact SoyKB team for any questions.


            MSMC

            USB 40X

    Only for logged in users. Please log in first.

            USB 15X

    Only for logged in users. Please log in first.


    * Note: This tool loads results files directly from iPlant data store. Some files may be temporarily inaccessible during the time of iPlant maintenance. Please re-access the link after the maintenance is complete or contact SoyKB team for any questions.


            MSMC

            USB 40X

    Only for logged in users. Please log in first.

            USB 15X

    Only for logged in users. Please log in first.


    * Note: This tool loads results files directly from iPlant data store. Some files may be temporarily inaccessible during the time of iPlant maintenance. Please re-access the link after the maintenance is complete or contact SoyKB team for any questions.


            MSMC

            USB 40X

    Only for logged in users. Please log in first.

            USB 15X

    Only for logged in users. Please log in first.


    * Note: This tool loads results files directly from iPlant data store. Some files may be temporarily inaccessible during the time of iPlant maintenance. Please re-access the link after the maintenance is complete or contact SoyKB team for any questions.


            MSMC



    Choose Position Range:

    Start Position End Position




            USB 40X

    Only for logged in users. Please log in first.

            USB 15X

    Only for logged in users. Please log in first.


    * Note: This tool loads results files directly from iPlant data store. Some files may be temporarily inaccessible during the time of iPlant maintenance. Please re-access the link after the maintenance is complete or contact SoyKB team for any questions.


            MSMC



    Choose Position Range:

    Start Position End Position




            USB 40X

    Only for logged in users. Please log in first.

            USB 15X

    Only for logged in users. Please log in first.


    * Note: This tool loads results files directly from iPlant data store. Some files may be temporarily inaccessible during the time of iPlant maintenance. Please re-access the link after the maintenance is complete or contact SoyKB team for any questions.


            MSMC




            USB 40X

    Only for logged in users. Please log in first.


            USB 15X

    Only for logged in users. Please log in first.



    * Note: This tool loads results files directly from iPlant data store. Some files may be temporarily inaccessible during the time of iPlant maintenance. Please re-access the link after the maintenance is complete or contact SoyKB team for any questions.


            MSMC

            USB 40X

    Only for logged in users. Please log in first.

            USB 15X

    Only for logged in users. Please log in first.

    Coming Soon

    Coming Soon