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+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
+