minibwa/minibwa_index

alignment

indexing

minibwa

BWA

BWA-MEM

reference

Description

Build a minibwa index (2-bit encoded sequence and BWT/suffix array) from a
reference FASTA file, for use with minibwa_map. Optionally also builds a
bisulfite (BS-seq) index for directional bisulfite sequencing alignment.

Type

bash_script

License

GPL-2.0-or-later

Keywords

alignment

indexing

minibwa

BWA

BWA-MEM

reference

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.minibwa_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/minibwa/minibwa_index/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--input	file required	Input reference FASTA file to be indexed.

Name

Type & Properties

--input

file

required

Output

Name	Type & Properties	Description
--output	file output	Output directory containing the minibwa index files (`.l2b`, `.mbw`, and `.meth.mbw` when `--meth` is used).

Name

Type & Properties

--output

file

output

Options

Name	Type & Properties	Description
--prefix	string	Prefix of the index files. Default is the same as the input FASTA file name.
--low_memory -l	boolean_true	Use a low-memory GPL'd algorithm for BWT construction, trading performance for reduced memory use.
--block_size -b	string	Block size, effective only when `--low_memory` is set. Default: '10m'.
--random_seed -s	integer	Random seed used to resolve ambiguous bases. Default: 11.
--sa_sample_rate -u	integer	Suffix array sample rate, at a rate of `1/(1<<INT)`. Default: 4.
--meth	boolean_true	Additionally build a bisulfite (BS-seq) FM-index (`.meth.mbw`).

Name

Type & Properties

--prefix

string

--low_memory

-l

boolean_true

--block_size

-b

string

--random_seed

-s

integer

--sa_sample_rate

-u

integer

--meth

boolean_true