Program Name: integron_gene_fetch
Version: 1.0
Developer: Yu-Wei Wu <yuwwu@indiana.edu>, Mina Rho <mrho@indiana.edu>, Thomas G. Doak <tdoak@indiana.edu>, and Yuzhen Ye <yye@indiana.edu>
Affiliation: School of Informatics and Computing, Indiana University

>> INTRODUCTION
The program is developed to get integron genes from metagenomic sequencing reads. It is capable of getting the integron mobile genes more efficiently, as these genes are extremely difficult to be detected in whole-genome assembly.  By assembling the dataset and traces all potential paths between any two contigs that consist of recombination sites, the integron_gene_fetch tool is able to get more integron genes given a pre-determined set of recombination site sequences.


Website:
  http://omics.informatics.indiana.edu/integron/

>> INSTALLATION
This program requires several different assisting programs, including SOAPdenovo, FragGeneScan, BWA, and cd-hit. Please download the programs from corresponding websites provided as follows.

SOAPdenovo (63mer or 127mer version)
  http://soap.genomics.org.cn/soapdenovo.html
FragGeneScan
  http://omics.informatics.indiana.edu/FragGeneScan/
BWA
  http://omics.informatics.indiana.edu/FragGeneScan/
cd-hit
  http://cd-hit.org/

Please also enter the directory integron_trace and type "make" to compile the program. The required program file will be created in this directory.

>> EXECCUTING integron_gene_fetch

perl get_integron_genes.pl
        -pair1 (paired-end file 1)
        -pair2 (paired-end file 2)
        -single (singleton file)
        -recomb (recombination consensus sequence file)
        [-kmer_len (de novo assembly kmer. default 39)]
        [-SOAPdenovo (location of SOAPdenovo program. default SOAPdenovo63mer)]
        [-BWA (location of BWA program. default bwa)]
        [-FragGeneScan (location of FragGeneScan program. default run_FragGeneScan.pl)]
        [-cdhit (location of cd-hit program. default cd-hit)]
        [-out (Output file header. Default integron_out)]

example:
(Assume that the paired-end and singleton files are 1.fa, 2.fa, and single.fa. Also assume that the recombination sites sequence file is attC.fa)

- Assume that all assisting programs can be executed by default settings
  perl get_integron_genes.pl -pair1 1.fa -pair2 2.fa -single single.fa -recomb attC.fa -out out

- Assume that cd-hit and SOAPdenovo executable need to be specified
  perl get_integron_genes.pl -pair1 1.fa -pair2 2.fa -single single.fa -recomb attC.fa -SOAPdenovo /bin/SOAPdenovo/SOAPdenovo63mer -cdhit /use/bin/cd-hit/cd-hit -out out