hisat2-alignment

What problem does it solve?

This Skill enables fast and memory-efficient RNA-seq alignment using HISAT2, ideal for bulk RNA-seq pipelines and small-genome RNA-seq projects.

Core Features & Use Cases

• Splice-aware Alignment: Achieves high sensitivity for transcriptome assembly.
• Memory Efficiency: Ideal for use with small genomes and large datasets.
• Use Case: When aligning RNA-seq reads to a reference genome for transcriptome analysis, this Skill is a preferred choice over alternatives like STAR due to its speed and memory usage.

Quick Start

Build a HISAT2 index and align reads using the following command:

hisat2 -p 16 --dta -x genome_hs2 -1 reads_R1.fq.gz -2 reads_R2.fq.gz -S sample1.sam