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.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input | file required | Input reference sequences in FASTA format. Can be a comma-separated list of files. |
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. |
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. |
Input Format Options
Name | Type & Properties | Description |
|---|---|---|
--fasta | boolean_true | Reference files are FASTA (default). |
--cmdline | boolean_true | Reference sequences given on command line. |
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 v0.4.1 \
-main-script target/nextflow/bowtie2/bowtie2_build/main.nf \
-params-file params.yaml Relationships
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Current component
bowtie2/bowtie2_buildbiobox v0.4.1
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