Mahika Kadam
Bioinformatics Scientist @ ASRT, Inc. | Bioinformatics data analysis and development
- Role
- Bioinformatics Scientist at ASRT, Inc.
- Location
- Austin, TX, US
- LinkedIn followers
- 500 followers
About Mahika Kadam
A dedicated Bioinformatics Scientist with a strong passion for leveraging data analysis…
Experience
Bioinformatics Scientist
Jul 2022 — Present · Austin, TX, US
Enhanced an existing pipeline that identifies unique kmers of bacterial organisms by adding features for genetic content analysis of genomes, customized the script to accommodate viral genomes, and successfully pushed these modifications to GitHub. Additionally, developed a Python script that utilizes Python classes to process intermediate pipeline output, generating gene names for the final kmers. Built a conda package for the pipeline and uploaded it to the ABiL conda channel.• Conducted comprehensive sequence analysis across samples to evaluate antimicrobial resistance (AMR) activity. Assessed tetracycline resistance by comparing sample sequences to established tetM gene references, discerning subjects exhibiting resistance. Additionally, employed pairwise comparison via BLAST with client-provided partial tetM amino acid sequences to confirm tetracycline resistance presence.• Performed end-to-end bioinformatics analysis for bacterial strains for in house and regional isolates, including executing Kraken and quality control (QC) processes, utilizing Fastp for data preparation, assembling sequences with SPAdes, assessing assembly quality through Quast, determining taxonomy with GTDB-Tk evaluating genome completeness using CheckM, and performing Average Nucleotide Identity (ANI) calculations. The steps were also compiled in a Nextflow pipeline.
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