Scribd Logo
Upload

Welcome to Scribd!

  • 161 views

    BPGA User Manual

    Uploaded by

    JML
    BPGA is a pipeline for bacterial pan-genome analysis. It can process outputs from clustering tools like USEARCH, CD-HIT and OrthoMCL to analyze bacterial gene pools. The pipeline performs functions like pan-genome profiling, core genome analysis, phylogenetic tree building, and functional annotation. It has a graphical user interface and provides results like core/pan plots, gene family distributions, and representative sequences for functional gene families.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd

    BPGA User Manual

    Uploaded by

    JML
    161 views9 pages
    BPGA is a pipeline for bacterial pan-genome analysis. It can process outputs from clustering tools like USEARCH, CD-HIT and OrthoMCL to analyze bacterial gene pools. The pipeline performs functions like pan-genome profiling, core genome analysis, phylogenetic tree building, and functional annotation. It has a graphical user interface and provides results like core/pan plots, gene family distributions, and representative sequences for functional gene families.

    Copyright

    © © All Rights Reserved

    Available Formats

    PDF, TXT or read online from Scribd

    Did you find this document useful?

    Is this content inappropriate?

    BPGA is a pipeline for bacterial pan-genome analysis. It can process outputs from clustering tools like USEARCH, CD-HIT and OrthoMCL to analyze bacterial gene pools. The pipeline performs functions like pan-genome profiling, core genome analysis, phylogenetic tree building, and functional annotation. It has a graphical user interface and provides results like core/pan plots, gene family distributions, and representative sequences for functional gene families.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    161 views9 pages

    BPGA User Manual

    Uploaded by

    JML
    BPGA is a pipeline for bacterial pan-genome analysis. It can process outputs from clustering tools like USEARCH, CD-HIT and OrthoMCL to analyze bacterial gene pools. The pipeline performs functions like pan-genome profiling, core genome analysis, phylogenetic tree building, and functional annotation. It has a graphical user interface and provides results like core/pan plots, gene family distributions, and representative sequences for functional gene families.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    You are on page 1of 9

    BPGA: Bacterial Pan Genome Analysis Pipeline

    User Manual

    Developed by: Narendrakumar M. Chaudhari1, Vinod Kumar Gupta1 & Chitra Dutta*
    Structural Biology & Bioinformatics Division, CSIR- Indian Institute of
    Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India

    Mailing addresses: NMC: naren.niper@gmail.com


    VKG: vinodgupta299@gmail.com
    CD: cdutta@iicb.res.in, cdutta.iicb@gmail.com

    1
    NMC & VKG contributed equally to this work.
    *
    Corresponding author

    Keywords: Bioinformatics, Pan-genome Analysis, Comparative Genomics

    Address of the Corresponding Author:


    Structural Biology & Bioinformatics Division, CSIR-Indian Institute of Chemical Biology,
    4, Raja S. C. Mullick Road, Kolkata 700032, India
    E-mail: cdutta@iicb.res.in, cdutta.iicb@gmail.com
    Phone: 91 33 2499 5812, Fax: 91 33 2472 3967, 91 33 2473 5197
    Description
    BPGA is a perl based pipeline to exploit protein clustering data for complete pan-
    genome analysis of bacterial species. BPGA can process outputs of three major
    clustering tools (USEARCH, CD-HIT and OrthoMCL) to obtain pan-genome profiles of
    bacterial gene pools.

    Availability:
    http://sourceforge.net/projects/bpgatool/
    http://www.iicb.res.in/bpga/index.html
    Installation
    Installation of BPGA is simple.
    1. Download the installer for Windows or LINUX system from our sourceforge page:
    http://sourceforge.net/projects/bpgatool/
    2. Run the installer as Administrator. It will extract files to a folder locally.
    Executables are present inside bin folder.
    3. BPGA is written in perl but bundled in an executable; hence no modules are
    needed to be installed.
    (For using BPGA as perl code, user should install required perl modules
    manually)
    Win32::GUI (For Windows only)
    Prima (For Linux only)
    Term::ANSIScreen
    File::chdir
    File::Remove
    Sort::Fields
    Statistics::Basic
    Statistics::Descriptive
    Bio::Phylo
    Data::Dumper

    Other requirements
     Installation of gnuplot (4.6.6) is must for plotting graphs. You can
    download Windows 32-bit version from here and 64-bit version from here.
    Linux users can install gnuplot from terminal by command:
    sudo apt-get install gnuplot-4.6.6
    Installation of ps2pdf (ghostscript ) is must for proper plotting by
    command:
    sudo apt-get install ghostscript
     BPGA uses USEARCH as a default clustering tool. Users need to get
    their own licensed Windows/Linux version freely available at:
    http://www.drive5.com/usearch/download.html,
    Note: 32 bit Version is freely available. It also works on 64 bit system.
    rename it to usearch.exe (for Windows) or usearch (for Linux) and copy it
    inside the bin folder.
    Note: For USERACH to work properly on Windows, please check the
    required vcomp100.dll system file inside Windows\System32 or
    System64 folder of your computer. If not, put it in this place. It is
    available at: http://www.drive5.com/usearch/manual/vcomp100.html
    .
     MUSCLE is used for alignments and tree generation. It is provided with
    the package.
     rsvg-convert.exe is required to handle SVG image data. It is also
    provided with the BPGA package.
    This is not available for Linux system. To run rsvg-convert.exe on Linux
    system install wine by command:
    sudo add-apt-repository ppa:ubuntu-wine/ppa -y && sudo
    apt-get update && sudo apt-get install wine

    Steps for run


    BPGA is easy, user friendly command line interface and it’s better to run it
    through command line/terminal.

     Option-1 (INPUT PREPARATION FOR CLUSTERING): Allows user to


    prepare input for clustering using different type of sequence files. User can
    select multiple files from file selection dialog. Allowed formats are *.faa (NCBI
    protein FASTA), *.pep.fsa (HMP protein FASTA) or any protein FASTA file
    and *.gbk/*.gb (genbank file). It will generate a single sequence file
    INPUT_all.faa, which will be used for clustering. List of organisms will be
    written to the list file. Dataset.xls will bear organism details for reference.

    Note: BPGA treats separate files as separate organism. If there are multiple files
    (chromosomes) for an organism, user should concatenate all files into a single file
    for that organism (applicable for all formats).

    All the files for a particular dataset should maintain uniform formats. User cannot
    use genebank files for some organisms and FASTA files for others. But user can
    use protein FASTA files of any type together (Using Any Protein FASTA File
    option of Input Preparation step)

     Option-2 (DEFAULT PAN GENOME ANALYSIS): Allows user to perform


    Pan-genome analysis on the data by clustering with USEARCH or by
    processing pre-clustered data by CD-HIT or OrthoMCL.

    Please note that, user must use input file (INPUT_all.faa generated by
    Option-1) for clustering with CD-HIT (online server/offline package) or with
    OrthoMCL pipeline with desired options.

    CD-HIT Web Server is available at: http://weizhongli-lab.org/cdhit_suite/cgi-


    bin/index.cgi?cmd=cd-hit . User is free to set parameters as desired.

    While clustering with USEARCH, identity cut off can be set by the user (see
    picture below).

     Option-3 (ONE CLICK MODE): Allows user to perform all the analyses in
    single step using all default parameters :
     Clustering: USEARCH (Identity cut off = 50%)
     No. of combinations: 30 for less than 20 genomes and 20 for 20-50
    genomes.
     Atypical GC Content Analysis: 2 × δ (Standard Deviation)
     Type of phylogeny tree: Neighbor Joining Tree (NJ).
     KEGG/COG Functional analysis: will be performed if dataset
    contains less than 50 genomes.
     Subset Analysis: NA
    In the next step, after completion of DEFAULT PAN GENOME ANALYSIS,
    ADVANCED ANALYSIS OPTIONS will be available.

    User may perform any of the 5 analyses one by one. Completion status of each
    analysis will be displayed in brackets ( _NOT DONE_ or _DONE_ ).
    After completing desired analyses, user should exit by typing ‘exit’’ and then
    closing the terminal.

    For MLST analysis, BPGA will halt and allow the user to make required changes.
    For MLST analysis, on user defined housekeeping genes Check "mlst_core.txt"
    for gene details and copy the respective cluster IDs from the first column to
    "CORE_MLST.txt". If you Press enter to continue without this step, 20 random
    clusters will be used for core phylogeny.

    Results
    Input preparation option will give input files (INPUT_all.faa, INPUT_all.ffn)
    necessary for clustering and dataset file (DATASET.xls) containing organism
    details. A file list, required for further analysis is also generated.

    The default analysis will give simple pan/core plot (Default_Core_Pan_Plot.pdf),


    distribution of gene families (Histogram.pdf), number of new genes added
    (New_Genes_Plot.pdf), genome wise statistics (stats.xls), representative sequences
    for core, accessory and unique gene families (REPSEQ_*.txt) and tab delimited
    pan-matrix (matrix.txt).
    Advanced options:
    1. Pan-core plot with combinations will give core and pan genome boxplot
    (Core_Pan_Plot.pdf ) and dot plot (Core_Pan_Dot_Plot.pdf ) generated using
    desired number of unique combinations of genomes.
    2. Phylogeny trees based on pan-matrix (Pan_phylogeny.pdf ) and core/MLST
    gene/protein sequences (Core_phylogeny.pdf ) will be generated. Respective *.ph
    files are provided for user to visualize using TreeView
    (http://taxonomy.zoology.gla.ac.uk/rod/treeview.html) and *.nwk files are also
    available for user to visualize using TreeGraph2 (http://treegraph.bioinfweb.info/).
    3. Atypical GC analysis will give sequences of core, accessory and unique genes
    with atypical (extreme) GC content (*_genes_with_atypical_GC_content.txt).
    4. Subset analysis will give default results for each group in separate folder. Group
    specific genes are present in groups_specific_genes.txt.
    5. Functional analysis will give COG and KEGG distribution of the core, accessory
    and unique gene families based on representative sequences
    (COG_DISTRIBUTION.pdf, COG_DISTRIBUTION_DETAILS.pdf,
    KEGG_DISTRIBUTION.pdf, KEGG_DISTRIBUTION_DETAILS.pdf ).
    COG and KEGG assignments for representative sequences are also provided.
    (*_COG_hits3.txt and *_KEGG_hits3.txt )

    Additional instructions
    For subset analysis user must create a text file having information about groups to
    be created. Here is the example,
    Organism ID as
    per dataset list
    Group 1 1 2 3 4
    Group 2 6 7 8 9 13 15
    Group 3 5 10 11 12 14

    Here, rows represent groups. Each number represents a genome (refer list file
    created during preparation). Blue colored labels are just for representation
    purpose. Actual file should contain only tab delimited values. Maximum 10 groups
    can be formed. There should be no repeats or wrong id.
    Accepted file formats:

     GBK: Freshly downloaded Genbank files from NCBI or HMP databases.


     FAA: Freshly downloaded amino acid sequence files from NCBI database.

     PEP.FSA: Freshly downloaded amino acid sequence files from HMPDACC


    database.

    You might also like