LR50

LR50 is a pipeline for assessing the quality of insect transcriptomes.It requires Linux platform.

Please follow the instructions to install the packages.

$ tar -xzvf LR50-1.0.tar.gz

• Set shell environment variable:
  
  export INPARANOID=/path/to/inparanoid_4.1
  export LR50=/path/to/LR50-1.0


• And add $LR50/bin to system variable:
  PATH=$LR50/bin:$PATH


• Add BLAST+ bin directory to system variable:
  PATH=/path/to/BLAST+/bin:$PATH


• After the NetStart was installed, add bin directory to system variable:
  PATH=/path/to/netstart/bin:$PATH

$ calculating_LR50.pl -t < Transcriptomes.nucleotide.fa > -g < GenomeReferenceSpecie.protein.fa > \
                   -d < Database for transcriptome annotation >

Transcriptomes.nucleotide.fa: fasta formate.
     Transcriptome nucleotide sequences which you want to assess.

GenomeReferenceSpecise.protein.fa: fasta formate.
     Genome reference specie (GRS) is a close related specie whose genome had been sequenced and well annotated.

Database for transcriptome annotation: protein database.
     NR database or other database is used to annotate the transcriptome.

When program finished, the results are saved as two files, which are placed in the directory “LR50_out”:
     - summary.xls
     - Translation_pep.fasta

NOTE: Two steps in this pipeline are time consuming. One is the annotation, and another is inparanoid. To save time, you need set more cpu cores to accelerate the first step. For inparanoid, you need change this line in the inparanoid.pl file:
          $blastall = "blastall"; #Add -aN to use N processors
     to
          $blastall = "blastall -a4"; #Add -aN to use N processors
     to add the blast processors cores.