cutadapt

Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline

✂️ Trim sequencing adapters from NGS data automatically

Fred's metabarcoding pipeline with Nextflow

Modular FASTQ preprocessing pipeline for quality control (FastQC/MultiQC) and adapter trimming (Cutadapt/Trimmomatic) of NGS sequencing data

quick taxonomic assignment of Nanopore metabarding data

Reproducible NGS data analysis pipeline for SRA datasets, covering raw-read QC, adapter and quality trimming, post-trimming QC, MultiQC reporting, read alignment, BAM processing, and downstream analysis.

This repository contains the code pipeline I developed for Next Generation Sequencing (NGS) analysis during my internship at CSIR-IGIB, New Delhi. The project was completed under the guidance of Mr. Sunil Nagpal and Dr. Bhupesh Taneja. For detailed instructions and a better understanding of pipeline, please refer to the README.md file.

Metabarcoding analysis pipeline, using DADA2 and qiime2

Modular shell pipeline for adapter trimming, genome alignment to GRCh38, and chromosome-level read mappability profiling using Bowtie2 and SAMtools

Dockerized cutadapt

Traceable single-end FASTQ quality and adapter trimming with exact per-read accounting and before/after QC.

Cell-surface glycoRNA-based cancer detection.

Pipeline reproducible de bioinformática para secuenciación de amplicón ITS (DADA2, cutadapt, diversidad alfa/beta) — con tests automatizados y CI.

A reproducible RNA-Seq analysis pipeline for Staphylococcus aureus under antibiotic stress, utilizing Nextflow and Singularity. It involves genome mapping, read counting, and statistical analysis to identify differentially expressed genes (DEGs) and generates key visualizations.

Script to unzip, clean, assemble, and convert illumina pair-end fastq files in all subdirectories for 16S amplicon data (V3, V4 and V3-V4 regions).

Automated environmental DNA (eDNA) metabarcoding pipeline for converting NCBI SRA sequencing data into taxonomically annotated species tables.