MetaCSST: Metagemonic Complex Sequence Scanning Tool

I. Introduction
    Metagenomic Complex Sequencing Scanning Tool (MetaCSST) is a tool to predict DGRs in sequenced genomes as well as metagenomic datasets. It is based on Generalized Hidden Markov Model (GHMM), using motif patterns to identify the elements in DGRs

II. Installation
    MetaCSSTmain and MetaCSSTsub are executable programs. If you want to modify the codes and recompile:
    g++ -lpthread src/main.cpp -o MetaCSSTmain_new
    g++ -lpthread src/sub.cpp -o MetaCSSTsub_new

III. Toolkit
    This system is zipped in one file,MetaCSST.tgz. The important files inside this tar file are listed here.
    |-MetaCSSTmainexecutable program to predict DGRs
    |-MetaCSSTsubexecutable program to identify TRs, VRs or RTs
    |-arg(/TR/VR/RT).configconfig files in the GHMM
    |-align/*alignalign matrix used to develop the GHMM
    |-main.cppsource code to build MetaCSSTmain
    |-sub.cppsource code to build MetaCSSTsub
    |-ghmm.h & fun.hsome functions, structures and objects
    |-callVR.plused to search VRs according to the raw GTF file generated by MetaCSSTmain
    |-removeRepeat.plremove identical TR-VR pairs generated by
    |-chomp.plpreprocess the input file in FASTA format
    |-addition/merged*collected DGRs
    |-addition/trainingtraining set
    |-addition/testtest set
    |-addition/classifyclassification of TRs/VRs/RTs, generated by MUSCLE
    |-example and a example to identify DGRs
    |-callORF.plscript to call Open Reading Frames
    |-coden.txtcoden table uesd to call ORFs

IV. Datasets
    All datasets mentioned in paper are provided here. V. Supplementary Data
     VI. Supplementary Tables
Please cite the following paper if you use MetaCSST.
"Discovery and characterization of the evolution, variation and functions of Diversity-Generating Retroelements using thousands of genomes and metagenomes", 2019, BMC Genomics , 20:595.

If you have any questions, feel free to contact us.
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Please send your comments or bug reports to Dr. Wei .