PRERANA J KOTI

APPLICATIONS EXTENSIVELY WORKED ON:
 Denovo DNA analysis (WGS)
 DNA Resequencing (Exome/WGS)
 Denovo RNA Sequencing
 RNA Resequencing
 Metagenome
 Whole Metagenome
 Small RNA (miRNA)
 WGBS

 ChIP Sequencing

Whole Genome Sequencing of Prokaryotes and Eukaryotes:

• Comparative Genomics, Phylogeny and Resistance Analysis with respect to bacterial genomes
• Assessing Probiotic and pathogenomics potential from whole genome assembly of bacteria

Whole Exome /Targeted Exome Analysis:

• Identifying the SNP, Indel and MNV using GATK and different pipelines Annotations by using Annovar and different tools Variant Effect Prediction and it's clinical correlation
• Mitochondrial data analysis and annotation CNV and SV analysis

Whole Genome Metagenomics and 16S rRNA Analysis:

• Mitochondrial Genome Assembly, Gene Rearrangement and Phylogeny Analysis
• Proficient in Developing Workflow for NGS Data Analysis

RNA Resequencing Analysis of Prokaryotes and Eukaryotes:

• Expression Profiling and Differential Gene Expression Analysis with respect to RNA Seq Gene Enrichment Analysis, Functional Annotations and it's Significant Biology Analysis

Denovo Transcriptome Analysis of Prokaryotes, Fungi and Eukaryotes:

• Expression Profiling and Differential Gene Expression Analysis with respect to RNA Seq Gene Enrichment Analysis, Functional Annotations and it's Significant Biology Analysis

BIOINFORMATICS SKILLS:

• Expertise in mining information from different Biological Database: NCBI, RefSeq, UniProtKb/SwissProt, PDB, InterPro, NRDB, BioDBnet, DAVID, KEGG, Panther, Ensembl, VEP, ANNOVAR, ClinVar, dbSNP, SRA, OMIM, Cosmic, UCSC, ExAC, 1000 genomes etc
• Open Source Bioinformatics Tools Hands on Experience: Fastqc, Fastqc Screen, NGS toolkit, FastX Toolkit, Fastp, Cutadapt, Trim Galore, Tophat, Hisat, Star, Cufflinks, StringTie, Cuffmerge, Cuffdiff, FeatureCounts, DESeq, Spades, Velvet, Unicycler, SSPACE, Soap Denovo, RNAmmer, barrnap, Augustus, Bowtie, BWA, PROKKA, GATK, Trinity, CD-HIT, Kallisto, RSEM, Java Treeview, Cluster3, CPC, iseeRNA, Mosdeph, Cytoscape, Qiime, Uparse, Samtools, VarScan, Qualimap, IGV, bedtools, bcftools
• Comfortable working with nextflow pipeline, conda, bioconda, biopython and docker packages

PROGRAMMING:
Operating System Concepts and Linux Environment :

• Linux commands (Navigation and Directory Control Commands, File Maintenance Commands, Display Commands, Print Commands etc , working with the files, file attributes, pipes, working with basic editors (nano, vi, emacs), Basic regular expressions, string search applications using regular expressions, Remote Computing & working On Remote Servers and also Microsoft Office skills

Awk-Shell scripting:

• String Functions, String Functions, Mathematical Functions, User – Defined Functions, Using System commands in awk, Applications, awk and grep, sed

Python:

• Introduction to statements, Types – Input / Output statements, conditional statements, looping, and jumping statements

R-Programming:

• Summarizing and exploring data, reading data from external files, Storing data to external files, Creating and storing R workspace, Manipulating objects in R: Mathematical operations, Basic matrix computation, Textual operations, Basic graph