GenotrickA pipeline for whole genome assembly and annotation of Genomes



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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.