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Map HISAT2 Specifications

Process Details

  • Name: Map HISAT2
  • Process UUID: 20bdceee-ed05-11e8-9ce4-85221b21564c
  • Process Group: Alignment

Overview

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) against the general human population (as well as against a single reference genome). This process performs high-throughput sequence alignment of FASTQ reads to a reference genome using the HISAT2 aligner, supporting both single-end and paired-end sequencing data.

This process is implemented in Bash, utilizing HISAT2 for alignment and SAMtools for BAM file conversion and statistics generation.

Key Functionality

  • High-speed alignment: Maps sequencing reads to reference genomes using HISAT2's graph-based alignment algorithm
  • Flexible input handling: Supports both single-end and paired-end sequencing reads with automatic detection
  • Quality assessment: Generates alignment statistics and flagstat reports for quality control
  • Output optimization: Converts SAM files to compressed BAM format and removes intermediate files

Input/Output Specification

Inputs

Required Inputs

  • reads

    • Description: FASTQ sequencing files containing the reads to be aligned
    • Format: FASTQ

  • hisat2Index

    • Description: Pre-built HISAT2 index files for the reference genome
    • Format: Index files

  • mate

    • Description: Specifies whether reads are single-end or paired-end
    • Format: Value (single/pair)

Outputs

  • mapped_reads

    • Description: Aligned reads in binary format
    • Format: BAM

  • outputFileTxt

    • Description: Alignment summary statistics and flagstat reports
    • Format: TXT

  • outputFileOut

    • Description: Additional alignment output files
    • Format: OUT

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • HISAT2 parameters
    • Description: Specify HISAT2 parameters
    • Default value: -p 4

References & Resources

  • Tool Documentation: HISAT2 official documentation
  • Related Papers: Kim, D., Paggi, J.M., Park, C., Bennett, C. and Salzberg, S.L. (2019) Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature Biotechnology, 37, 907-915. DOI: 10.1038/s41587-019-0201-4