bradylab / iggpipe

IGG marker pipeline

IGGPIPE

To view README on your computer, open README.html in a browser. It will show the IGGPIPE version number above. File README.asciidoc is meant to be viewed on GitHub and does not show the version number. File Version.txt also has the version number.

The BradyLab/IGGPIPE GitHub repository contains code and documentation for the software package called IGGPIPE (Indel Group in Genomes Pipeline).

IGGPIPE analyzes two or more genomes for length-polymorphic regions bounded by unique sequences and designs PCR primers within these sequences. The primers can be used to amplify the region from genomic DNA of any of the species used to create the markers, and the amplicon size will indicate which species the DNA came from - an IGG marker.

Download, Installation, and Running

Requirements

• Installation has been tested on 64-bit Mac OSX, 64-bit Linux, and 64-bit Windows. It will not work on 32-bit systems (due to dependency on Jellyfish2).

• See the INSTALL document section Detailed Installation Instructions Part 4: Install prerequisite applications for instructions to install these required programs:

  1. Xcode (V6.4 works) (Apple App Store; make and g++)

  2. Jellyfish V2 or later (V2.2.3 works) (http://www.genome.umd.edu/jellyfish.html)

  3. Perl V5 or later (V5.16.0 works) (https://www.perl.org/get.html)

  4. R V3 or later (V3.2.1 works) (https://www.r-project.org)

  5. Primer3 (V2.3.6 works) (http://sourceforge.net/projects/primer3)

  6. NCBI e-PCR (V2.3.12-1 works) (http://www.ncbi.nlm.nih.gov/tools/epcr)

  7. MUSCLE (V3.8.31 works) (http://www.drive5.com/muscle/downloads.htm)

Download IGGPIPE files

1. Browse to https://github.com/BradyLab/IGGPIPE

2. Click the "Clone or download" button at the right side of the screen near the top

3. Select Download ZIP, then choose a place to put it on your computer

   Note	Alternatively, you can clone the git repository with this command line command:

   git clone https://github.com/BradyLab/IGGPIPE.git

4. Unzip the zip file on your computer.

5. Rename the unzipped folder from "IGGPIPE-master" to just "IGGPIPE".

Install IGGPIPE

• Look inside the downloaded IGGPIPE folder on your computer for file INSTALL.html, open it, and follow the instructions.

Run IGGPIPE to generate markers after installation

• Find file RUN.html in the IGGPIPE folder on your computer, open it, and follow the instructions.

For problems and help:

• Post an issue on GitHub under BradyLab/IGGPIPE repository

• Contact me, Ted Toal, [email protected]

References

Please cite the following paper when using IGGPIPE software:

• Toal, Ted, Diana Burkart-Waco, Tyson Howell, Mily Ron, Sundaram Kuppu, Anne Bagg Britt, Roger T. Chetelat, and Siobhan M. Brady. "Indel Group in Genomes (IGG) Molecular Genetic Markers." Plant Physiology (2016): pp-00354.

iggpipe's Issues

Error running IGGPIPE test data: jellyfish::compacted_hash::ErrorReading

I have installed IGGPIPE in Ubuntu 14.04 lts workstation following the guides of IGGPIPE instructions. While running test data, it throws error. Following is the log file:

getSeqInfo file(s) for genome(s) ALL are up to date.

getKmers file(s) for genome(s) ALL are up to date.

*** getKmers PARAMS=allParameters.test GENOME=1 ***
Extracting unique 11-mers from testFASTA/ITAG2.4_test.fasta into binary file outTestHP11/Kmers/Kmers_1.kmers
(time
jellyfish count -C -m 11 -s 80M -U 1 -o outTestHP11/Kmers/Kmers_1.kmers testFASTA/ITAG2.4_test.fasta ) 2>&1 ### getKmers_1
1.12user 0.02system 0:01.14elapsed 100%CPU (0avgtext+0avgdata 45772maxresident)k
0inputs+3744outputs (0major+8060minor)pagefaults 0swaps
Finished.

*** kmersToText PARAMS=allParameters.test GENOME=1 ***
Converting 11-mers from binary file outTestHP11/Kmers/Kmers_1.kmers into text format in file outTestHP11/Kmers/Kmers_1.kmers.txt
(time
jellyfish dump -c -o outTestHP11/Kmers/Kmers_1.kmers.txt outTestHP11/Kmers/Kmers_1.kmers ) 2>&1 ### jellydump_1
terminate called after throwing an instance of 'jellyfish::compacted_hash::ErrorReading'
what(): 'outTestHP11/Kmers/Kmers_1.kmers': File truncated
Command terminated by signal 6
0.00user 0.00system 0:00.13elapsed 1%CPU (0avgtext+0avgdata 1696maxresident)k
0inputs+0outputs (0major+493minor)pagefaults 0swaps

Can you please troubleshoot this for me. I am not an expert Bioinformatics guy hence, I may require detailed advices to make the program work. Please help.