bowtie2/bowtie2_build

Alignment

Indexing

Description

Build Bowtie2 index files from reference sequences.

The Bowtie2 index is based on the FM Index of Ferragina and Manzini, which in turn
is based on the Burrows-Wheeler Transform. The algorithm used to build the index is
based on the blockwise algorithm of Karkkainen.

Type

bash_script

License

GPL-3.0

Keywords

Alignment

Indexing

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.bowtie2_index"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.0 \  
  -main-script target/nextflow/bowtie2/bowtie2_build/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	Input reference sequences in FASTA format. Can be a comma-separated list of files.

Name

Type & Properties

--input

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Directory where the index files will be written.
--index_name	string	Base name for the index files. If not provided, will use the input filename without extension.

Name

Type & Properties

--output

file

required

output

--index_name

string

Index Construction Options

Name	Type & Properties	Description
--large_index	boolean_true	Force generated index to be 'large', even if reference has fewer than 4 billion nucleotides.
--noauto	boolean_true	Disable automatic -p/--bmax/--dcv memory-fitting.
--packed	boolean_true	Use packed strings internally; slower, less memory.
--bmax	integer	Max bucket size for blockwise suffix-array builder.
--bmaxdivn	integer	Max bucket size as divisor of reference length.
--dcv	integer	Diff-cover period for blockwise (default 1024).
--nodc	boolean_true	Disable diff-cover (algorithm becomes quadratic).
--noref	boolean_true	Don't build .3/.4 index files.
--justref	boolean_true	Just build .3/.4 index files.
--offrate	integer	SA is sampled every 2^<int> BWT chars (default 5).
--ftabchars	integer	Number of chars consumed in initial lookup (default 10).
--seed	integer	Seed for random number generator.
--quiet	boolean_true	Suppress verbose output.
--verbose	boolean_true	Log the issued command.
--debug	boolean_true	Use the debug binary; slower, assertions enabled.
--sanitized	boolean_true	Use sanitized binary; slower, uses ASan and/or UBSan.

Name

Type & Properties

--large_index

boolean_true

--noauto

boolean_true

--packed

boolean_true

--bmax

integer

--bmaxdivn

integer

--dcv

integer

--nodc

boolean_true

--noref

boolean_true

--justref

boolean_true

--offrate

integer

--ftabchars

integer

--seed

integer

--quiet

boolean_true

--verbose

boolean_true

--debug

boolean_true

--sanitized

boolean_true

Input Format Options

Name	Type & Properties	Description
--fasta	boolean_true	Reference files are FASTA (default).
--cmdline	boolean_true	Reference sequences given on command line.

Name

Type & Properties

--fasta

boolean_true

--cmdline

boolean_true