trimmomatic

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

A 10x faster version base on official trimmomatic. The results of trimmomatic-pigz are exactly the same with official trimmomatic.

Whole Exome Sequencing end-to-end pipeline. Starting from whole exome fastq files: Data QC, Adapter Trimming, Reference Genome Alignment, SAM/BAM Validation, Data Recalibration and Variant Calling.

Quality Control, Mapping and Reads Count for RNA-Seq Analysis

A complete workflow for analyzing and visualizing bulk RNA-seq data.

Bulk Rna-seq Analysis

Step-by-step approach in the analysis of Rainbow trout DNA from raw reads to population insights using fastqc, trimmomatic, bwa, vcftools, plink, and R.

Single-end RNA-seq pipeline: FastQC → Trimmomatic → HISAT2 → featureCounts. 93.98% alignment rate.

An automated, end-to-end RNA-Seq preprocessing and quantification pipeline utilizing HISAT2 for genomic alignment and featureCounts for gene expression matrix generation. It is optimized for VMware.

Slurm scripts for analyzing bulk Cutandtag data

A contract‑driven HPC pipeline for FASTQ trimming using BBDUK or Trimmomatic, featuring strict preflight validation, explicit SLURM ABI propagation, deterministic tool installation, and restart‑safe per-sample execution.

RNA-seq code with Bowtie alignment and generating strain-specific counts using Emase

Whole Genome Sequencing analysis of Mycobacterium tuberculosis using Illumina Single-End reads from quality control to variant calling.

Back Up of Trimmomatic for learning and testing/modification. Find Original Code at: https://github.com/usadellab/Trimmomatic

Walks through installation and usage of FASTQC, MultiQC, Trimmomatic, and Salmon for transcriptomic data preprocessing. Includes Grid Engine shell scripts that can be looped over many files in a directory.

End-to-end E. coli Whole Genome Sequencing (WGS) pipeline using FastQC, Trimmomatic, BWA, SAMtools and BCFtools from raw FASTQ to variant calling.

RNA-seq analysis from FASTQ to differential gene-expression using open-source tools

Cell-surface glycoRNA-based cancer detection.

The repository contain directories of projects done during the bioinformatics degree program