CAPRG SUMMARY

“Contigs Assembly Pipeline using Reference Genome” (CAPRG) assemble long sequence reads for non-model organisms by leveraging a reference genome of a closely-related phylogenetic relative. With the advent of NGS, the assembling of millions of reads is computationally expensive. Various clustering method like megablast, cd-hit have been employed to reduce the memory and processing time. CAPRG utilizes mapping the raw reads of genome/transcriptome against a reference genome and then assembling them to longer contigs that can be utilized for "gene-hunting". The Pipeline consist of three step: 1. Map the transcriptome raw sequences against the reference genome 2. Store the mapped reads in RDBMS database 3. Assemble reads based on its chromosomal position

executables_11-11
bwaswCommand.sh
DBConsts.pm
Documentation.rtf
PrepareData.pl
RunCAPRG.pl