hisat2

Nextflow Alignment Pipeline - from fastq.gz to sorted bam/cram with ease

RNA-seq analyses.

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

Codes that I use for day-to-day work in lab.

SPEAQeasy: portable LIBD RNA-seq pipeline using Nextflow. Check http://research.libd.org/SPEAQeasy-example/ for an example on how to use this pipeline and analyze the resulting output files.

A complete bioinformatics pipeline (FastQC, fastp, HISAT2, featureCounts, DESeq2) for RNA-Seq DGE analysis of Klebsiella pneumoniae (WT vs. ΔcpxR).

Evaluating HISAT2, Salmon and Kallisto alignment using Checkpoint Blockade treated CT26 Experimental Data

These are tutorials on a subset of tools available for processing raw RNAseq data. This if for HISAT2_SAMtools_Stringtie_gffcompare_ballgown pipeline or HISAT2_SAMtools_Stringtie_PrepDEanalysis.py_DESeq2 pipeline

This repository houses the pipeline I coded to perform differential analysis of transcriptomes from two oyster species, C. gigas and C. virginica and isolate genes in the apoptosis pathway.

VAP : For Reference mapping and Variant detection.

Exact-output CPU and CUDA acceleration for HISAT-3N table generation, with reproducible ablations and correctness gates.

🧬 湿实验室友好的本地 RNA-seq 分析网页工具：一键安装，浏览器里完成 比对→差异基因→GO/KEGG 富集，数据不出本机 | Local-first RNA-seq web app for wet labs (Streamlit + WSL)

Scripts to index and align Bovine genome with HISAT2

Containerized Snakemake workflow for RNA-seq: HISAT2 + featureCounts gene counts, Salmon transcript quantification, and comprehensive QC (FastQC, fastp, Picard, Qualimap, RSeQC, MultiQC). On-demand index building; Docker & Apptainer ready.

A front-end GUI to map NGS DNA sequencing data using HISAT backend tool. This software offers robust seamless queueing of the mapping operations along with parameter memory for quick and easy customization.

R-based comparison of HISAT2 vs Bowtie2 alignment performance across RNA-Seq and WGS applications using chr21 reference and platform-representative simulated data; includes MAPQ-based SAM quality assessment.

End-to-end RNA-seq analysis pipeline — from raw FASTQ files to differential expression results. Python + R + DESeq2 + Streamlit.

snakemake files of the tuxedo v2 pipeline from Pertea et al 2016

Build Docker container for HISAT2 and (optionally) convert to Apptainer/Singularity.

End-to-end bulk RNA-seq analysis pipeline for HPC clusters (Nextflow + Snakemake) | QC → Trimming → Mapping → Quantification