This script demonstrates using shell scripting to provide an automatized and user-friendly scientific pipeline to perform variant calling and quasispecies reconstruction specifically for viral vaccine samples.
All requirements should be downloaded and installed by the user. As default the tools should be in path. Or in the 00_Exe folder
./v2ida.sh samples ref 1 10000 5
where: samples is the name of a .tab file containing the samples names
ref is the reference genome used for alignment (default: fasta format)
1 is the inicial nucleotide for quasispecies reconstruction
10000 is the final nucleotide for quasispecies reconstruction
5 is how many parts you would like to divide the genome for quasispecies reconstruction
This pipeline was developed by Andrade, AAS (aandrade@lncc.br) at the National Laboratory for Scientific Computing - Bioinformatic Laboratory (LABINFO)
ANDRADE, AAS; SOARES, AER; ALMEIDA, LGP; PESTANA, CP; AQUINO, CL; MEDEIROS, MA; VASCONCELOS, ATR. Testing the genomic stability of the Brazilian Yellow Fever vaccine strain using next-generation sequencing data. (IN PRESS)