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.
Input
Name | Type & Properties | Description |
|---|---|---|
--input | file required | Input reference FASTA file to be indexed. |
Output
Name | Type & Properties | Description |
|---|---|---|
--output | file output | Output directory containing the minibwa index files (`.l2b`, `.mbw`, and `.meth.mbw` when `--meth` is used). |
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`). |
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 Relationships
Used by
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Current component
minibwa/minibwa_indexbiobox v0.5.0
Uses
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