2020-07-11 11:42:13 +00:00
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name: HISAT2
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2020-03-20 11:04:25 +00:00
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description: Graph-based alignment of next generation sequencing reads to a population of genomes
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keywords:
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- Alignment
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- Short reads
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- graph FM Index (GFM)
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- RNA-seq
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tools:
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- fastqc:
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description: |
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HISAT2 is a fast and sensitive alignment program for mapping next-generation
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sequencing reads (whole-genome, transcriptome, and exome sequencing data)
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against the general human population (as well as against a single reference genome).
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Based on GCSA (an extension of BWT for a graph) it is designed and implemented as a
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graph FM index (GFM).
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homepage: http://daehwankimlab.github.io/hisat2/
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documentation: https://ccb.jhu.edu/software/hisat2/manual.shtml
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input:
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-
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- sample_id:
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type: string
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description: Sample identifier
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- reads:
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type: file
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description: Input FastQ file, or pair of files
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output:
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-
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- report:
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type: file
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description: mapping statistics report
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2020-07-11 11:54:12 +00:00
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pattern: "*hisat2_stats.txt"
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2020-03-20 11:04:25 +00:00
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- alignment:
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type: file
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description: alignment file in BAM format
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2020-07-11 11:54:12 +00:00
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pattern: "*hisat2.bam"
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2020-03-20 11:04:25 +00:00
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authors:
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2020-07-11 11:54:12 +00:00
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- "@FelixKrueger"
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