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agrima2010/README.md

Agrima Bhatt

LinkedIn GitHub Email

About

  • Bioinformatician with a double master's in Biotechnology (India) and Precision Medicine (Uppsala University, Sweden) with knowledge and experience of working in both wet-lab and dry-lab environments.

Tech

Nextflow · nf-core · Python · R · Bash · Linux/HPC · Docker · Git

Projects

nf-core/seqinspector — QC pipeline for sequencing cores

repo

Dedicated QC-only pipeline for sequencing data.

Contributions :

  • Development of the pipeline by adding subworkflows and QC modules such as Picard tools, SAMtools, BWA-MEM2, fastp, fqlint, Kraken2.
  • Wrote module tests and assisted in the pipeline release.

Selective Metagenomics through Adaptive Nanopore Sequencing

Significance: Adaptive sampling on Oxford Nanopore Technologies (ONT) platforms selectively sequence target molecules by alignment to a reference genome. This project aimed to replace the alignment step with a deep learning-based taxonomic classifier (BERTax), enabling enrichment of broad taxonomic groups rather than specific known organisms.

Currently

  • Contributing to nf-core/sarek modularization
  • Working on AI Automation workflows

Let's build something. → LinkedIn

Popular repositories Loading

  1. NGI-ONT_scRNAseq-tech_note-2025 NGI-ONT_scRNAseq-tech_note-2025 Public

    Forked from NationalGenomicsInfrastructure/NGI-ONT_scRNAseq-tech_note-2025

    Jupyter Notebook

  2. seqinspector seqinspector Public

    Forked from nf-core/seqinspector

    QC pipeline to inspect your sequences_abh

    Nextflow

  3. configs configs Public

    Forked from nf-core/configs

    Config files used to define parameters specific to compute environments at different Institutions

    Nextflow

  4. Master-s-Thesis-Selective-Nanopore Master-s-Thesis-Selective-Nanopore Public

    Selective metagenomics through adaptive nanopore sequencing

    Jupyter Notebook

  5. bertax_training bertax_training Public

    Forked from rnajena/bertax_training

    Training scripts for BERTax

    Python

  6. agrima2010 agrima2010 Public

    Hello World!