Software used in Genotrick
Genotrick have several dependencies. All software are freely available for scientific community.
Software to filter the short reads
First step in the Genotrik pipeline is to filter raw reads generated by sequencing machines. To filter the raw reads, we have incorporated
NGS QC pipeline, developed at
National Institute Of Plant Genome Research, India.
Software to assemble the sequencing reads
Whole genome assembly is the second step in Genotrick pipeline. Here, user should provide short reads to assemble in contigs. Several options are avilable for genome assembly. In Genotrick, we have incorporated
Velvet software for this purpose. Velvet was developed at
EMBL-EBI.
Software for whole genome annotation
Whole genome annotation is the last step in Genotrick pipeline. In this step, contigs or full chromosomes have been annotated, including, prediction of coding sequences (CDS's), rRNA and tRNA gene prediction. Here,
PROKKA software is incorporated in Genotrick. At this last step of Genotrick pipeline, annotated genome is produced in various file formats i.e. GFF3, GBK and SQN.