Requirements

HUPAN toolkit integrates more than 10 software, most of these software can be provided to the main program when the specific tool is selected. It is convenient for users to work on supercomputers or clusters. To run the main program of HUPAN toolkit, you only need several software and packages.

1. R 3.1 or later

R is utilized for visulization and statistical tests in HUPAN toolkit. Please install R first and make sure R and Rscript are under your PATH.

Download R here.

2. R packages

Several R packages are needed including ggplot2, reshape2 and ape packages. Follow the Installation step 3 or you can install the packages by yourself.

3. Perl
4. g++
5. Python 2.5, 2.6 or 2.7 (required by QUAST)

Installation procedures

1. Download the HUPAN toolkit here.

2. Uncompress the HUPAN toolkit package.

   tar zxvf HUPAN-vXX.XX.tar.gz

3. Install necessary R packages.

   cd HUPAN-vXX.XX
   Rscript installRPac

4. Compile the source codes.

   make

   You will find executable files:ccov,bam2cov and hupan et al. in bin/ directory.

5. Add bin/ to PATH and add lib/ to LD_LIBRARY_PATH.

   To do this, edit your path in the following text and add the text to the end of the file ~/.bash_profile

   export PATH=$PATH:/path/to/HUPAN/bin:
   export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/HUPAN/lib/:
   export PERL5LIB=$PERL5LIB:/path/to/HUPAN/lib/:
   source /path/to/HUPAN/hupan_cmd.sh

   and run

   source ~/.bash_profile

6. Test if HUPAN toolkit is installed successfully

   hupan

   If you could see the following content, congratulations! HUPAN toolkit is successfully installed. If not, see if all the requirements are satisfied; or you may contact the authors for help.

   Usage: hupan <command> ...
   
   Available commands:
           qualSta         View the overall sequencing quality of a large number of files
           trim            Trim or filter low-quality reads parallelly
           alignRead       Map reads to a reference parallelly
           sam2bam         Covert alignments (.sam) to sorted .bam files
           bamSta          Statistics of parallel mapping
           assemble        Assemble reads parallelly
           alignContig     Align assembly results to a referenece parallelly
           extractSeq      Extract contigs parallelly
           assemSta        Statistics of parallel assembly
           getUnalnCtg     Extract the unaligned contigs from nucmer alignment (processed by quast)
           rmRedundant     Remove redundant contigs of a fasta file
           pTpG            Get the longest transcripts to represent genes
           geneCov         Calculate gene body coverage and CDS coverage
           geneExist       Determine gene presence-absence based on gene body coverage and CDS coverage
           subSample       Select subset of samples from gene PAV profile
           gFamExist       Determine gene family presence-absence based on gene presence-absence
           bam2bed         Calculate genome region presence-absence from .bam
           fastaSta        Calculate statistics of fasta file
           sim             Simulation and plot of the pan-genome and the core genome
           getTaxClass     Obtain the taxonomic classification of sequences
           rmCtm           Detect and discard the potentail contamination
           blastAlign      Align sequences to target sequence by blast
           simSeq          Simulate and plot the total size of novel sequences
           splitSeq        Split sequence file into multiple small size files
           genePre         Ab initio gene predict combining with RNA and protein evidence
           mergeNovGene    Merge maker result from multiple maker result files
           filterNovGene   Filter the novel precited genes.