name: HISAT2
description: Graph-based alignment of next generation sequencing reads to a population of genomes
keywords:
    - Alignment
    - Short reads
    - graph FM Index (GFM)
    - RNA-seq
tools:
    - fastqc:
        description: |
            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).
            Based on GCSA (an extension of BWT for a graph) it is designed and implemented as a
            graph FM index (GFM).
        homepage: http://daehwankimlab.github.io/hisat2/
        documentation: https://ccb.jhu.edu/software/hisat2/manual.shtml
input:
    -
        - sample_id:
            type: string
            description: Sample identifier
        - reads:
            type: file
            description: Input FastQ file, or pair of files
output:
    -
        - report:
            type: file
            description: mapping statistics report
            pattern: "*hisat2_stats.txt"
        - alignment:
            type: file
            description: alignment file in BAM format
            pattern: "*hisat2.bam"
authors:
    - "@FelixKrueger"