Genomic DNA extraction (blood, tissue, bacterial culture)
Metagenomic DNA extraction (rumen fluid, caecal, faecal, soil, etc.)
RNA extraction (tissues, viral culture)
Metatranscriptome extraction (rumen fluid)
PCR
qPCR
dPCR
Agarose gel electrophoresis
Agilent Bioanalyzer
Next-generation Sequencing (NGS) library preparation for Illumina and Ion Torrent platforms (Shotgun, Marker gene target, Ampliseq multi-targets, RNAseq, small RNA)
NGS run setup (Roche-454 GS-FLX, Ion Torrent PGM, Ion S5, Illumina MiSeq)
High-throughput genotyping on Affymetrix GeneTitan
Single cell suspension from tissue
Nuclei isolation
Processing single cell/nuclei with 10x Genomics platform
Primer designing
Sanger sequence analysis using online and offline tool/software (Linux/Window)
NGS data QC and pre-processing (Prinseq-lite Perl script, FastQC, Trimmomatic, Trim-galore, CutAdapt, PandaSeq)
De novo assembly (SPADes, CLC Genomics Workbench, GS de novo assembler, MIRA, Velvet, Celera Assembler, CISA)
Bacterial genome annotation (BLAST2GO, GenSAS, local BLAST, PROKKA, Anvi’o, JGI IMG/M, DRAM, METABOLIC, dbCAN2)
Reference based read mapping (STAR, BWA and bowtie2)
Variant prediction and annotation (Samtools, Freebayes, GATK, SnpEff)
Ribosomal marker gene analysis (QIIME, QIIME2, STAMP, MicrobiomeAnalyst, MetagenAssist, R-based DADA2 and Phyloseq)
Shotgun metagenomics and metatranscriptomics data analysis (SqueezeMeta, MG-RAST, MEGAN, EBI-MGnify, JGI IMG/M, MetaWRAP, Anvi'o)
RNA-Seq analysis (RNAseq pipeline within CLC Genomics Workbench, STAR for mapping and differential analysis using DESeq2 and Cufflinks work-flow)
Genotyping/microarray data analysis (Axiom analysis suite, PLINK, Gemma, GCTA)
Reduced Representation Bisulfite Sequencing (RRBS) data analysis (Bismark, MethylKit)
Single-cell RNAseq data analysis (Cellranger and Seurat)
I have used the tools written in Perl, Python, JAVA and R. Additionally, I am routinely writing scripts/programs in Bash, Perl and R, while I have working knowledge and comfortable with using Python scripts. I am comfortable with editing the scripts as well as troubleshooting with respect to installation of tools/pipelines including nextflow.