nf-core_modules/tools/umi_tools/dedup/dedup.yml

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1.3 KiB
YAML

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