hisat2/hisat2_build

Build

Index

RNA-seq

HISAT2

Description

Build a HISAT2 index from a reference genome FASTA file.
Optionally incorporates splice sites, exons, SNPs, and haplotypes for a graph-based index.

Type

bash_script

License

MIT

Keywords

Build

Index

RNA-seq

HISAT2

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
index_dir: "$id.$key.index_dir.index"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.5.0 \  
  -main-script target/nextflow/hisat2/hisat2_build/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--reference	file required multiple	Reference genome FASTA file(s). Provide multiple files to build an index from a combined multi-FASTA reference.

Name

Type & Properties

--reference

file

required

multiple

Annotation Inputs

Name	Type & Properties	Description
--ss	file	Splice site file in HISAT2 tab-separated format.
--exon	file	Exon file in HISAT2 tab-separated format.
--snp	file	SNP file for building a SNP-aware index.
--haplotype	file	Haplotype file for building a haplotype-aware index.

Name

Type & Properties

--ss

file

--exon

file

--snp

file

--haplotype

file

Outputs

Name	Type & Properties	Description
--index_dir	file required output	Directory where the HISAT2 index files will be written (.1.ht2 through .8.ht2).
--index_prefix	string required	Prefix name for the 8 index files inside the index directory.

Name

Type & Properties

--index_dir

file

required

output

--index_prefix

string

required

Index Construction Options

Name	Type & Properties	Description
--large_index	boolean_true	Force a large index (>4 billion nucleotides), even if the reference is smaller.
--noauto	boolean_true	Disable automatic selection of block size and memory parameters.
--nodc	boolean_true	Disable the difference-cover sample (may reduce memory usage at the cost of speed).
--noref -r	boolean_true	Do not build the packed reference (.3/.4.ht2) portion of the index.
--justref -3	boolean_true	Build only the packed reference (.3/.4.ht2) portion of the index.
--bmax	integer	Maximum number of suffixes allowed in a block during index construction. Default is auto-selected.
--bmaxdivn	integer	Set bmax as a fraction of the reference length (reference_length / bmaxdivn). Default is 4.
--dcv	integer	Period for the difference-cover sample. Larger values use less memory but slow construction. Default is 1024.
--offrate -o	integer	Suffix array is sampled every 2^N BWT characters. Larger values = smaller index but slower alignment. Default: 4.
--ftabchars -t	integer	Number of characters consumed in the initial lookup table (ftab). Default is 10.
--localoffrate	integer	Suffix array sampling rate for the local index: every 2^N BWT chars. Default: 3.
--localftabchars	integer	Number of characters consumed in the local initial lookup table. Default is 6.

Name

Type & Properties

--large_index

boolean_true

--noauto

boolean_true

--nodc

boolean_true

--noref

-r

boolean_true

--justref

-3

boolean_true

--bmax

integer

--bmaxdivn

integer

--dcv

integer

--offrate

-o

integer

--ftabchars

-t

integer

--localoffrate

integer

--localftabchars

integer

Other Options

Name	Type & Properties	Description
--seed	integer	Seed for the pseudo-random number generator.
--quiet -q	boolean_true	Disable verbose output (quiet mode).

Name

Type & Properties

--seed

integer

--quiet

-q

boolean_true