Hisat2

Fast and sensitive alignment of sequencing reads to a population of genomes

Citation

Citation: 10.1038/nmeth.3317

Environment

This tool uses the following conda environment:

Channels: - conda-forge - bioconda

Dependencies: - hisat2 - samtools

Installation

This tool will be automatically installed when first used:

library(ShennongTools)

# Tool will be installed automatically on first use
result <- sn_run("hisat2", "index", ...)

Available Commands

index

Build HISAT2 index from a reference genome FASTA file

Basic Usage:

result <- sn_run("hisat2", "index",
  # Add your parameters here
)

align

Align reads to reference genome and convert output to BAM

Basic Usage:

result <- sn_run("hisat2", "align",
  # Add your parameters here
)

Examples

Index Example

library(ShennongTools)

result <- sn_run("hisat2", "index",
  fasta = "sequences.fasta",
  index = "genome_index",
  threads = 8
)

# Check if successful
if (sn_is_toolcall_success(result)) {
  cat("Command completed successfully!\n")
} else {
  cat("Command failed. Check logs:\n")
  cat(readLines(result@log_file), sep = "\n")
}

Align Example

library(ShennongTools)

result <- sn_run("hisat2", "align",
  read1 = "sample_R1.fastq.gz",
  index = "genome_index",
  bam = "alignment.bam",
  threads = 4
)

# Check if successful
if (sn_is_toolcall_success(result)) {
  cat("Command completed successfully!\n")
} else {
  cat("Command failed. Check logs:\n")
  cat(readLines(result@log_file), sep = "\n")
}

Parameters Reference

index Parameters

Inputs:

Parameter	Type	Required	Description
`fasta`	fasta	Yes	Input reference genome FASTA file

Outputs:

Parameter	Type	Required	Description
`index`	prefix	Yes	HISAT2 index files basename prefix

Parameters:

Parameter	Type	Default	Description
`threads`	integer	8	Number of threads to use

align Parameters

Inputs:

Parameter	Type	Required	Description
`read1`	fastq	Yes	FASTQ file for read 1 or single-end reads
`read2`	fastq	No	FASTQ file for read 2 (for paired-end reads, optional)
`index`	prefix	Yes	Index filename prefix (minus trailing .X.ht2)

Outputs:

Parameter	Type	Required	Description
`bam`	bam	Yes	Output BAM file path

Parameters:

Parameter	Type	Default	Description
`threads`	integer	4	Number of threads to use