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