bwa/bwa_sampe
alignment
BWA
BWA-sampe
SAM
paired-end
Description
BWA sampe - generate paired-end alignment in SAM format from BWA aln SAI files.
Input
Name | Type & Properties | Description |
|---|---|---|
--index | file required | BWA index base name (prefix of .amb, .ann, .bwt, .pac, .sa files). |
--sai1 | file required | Input SAI file for first reads (R1) generated by BWA aln. |
--sai2 | file required | Input SAI file for second reads (R2) generated by BWA aln. |
--reads1 | file required | Input FASTQ file with first reads in pair (R1). |
--reads2 | file required | Input FASTQ file with second reads in pair (R2). |
Output
Name | Type & Properties | Description |
|---|---|---|
--output -f | file output | Output SAM file. If not specified, output goes to stdout. |
Pairing Options
Name | Type & Properties | Description |
|---|---|---|
--max_insert_size -a | integer | Maximum insert size. Default is 500. |
--max_occ_one_end -o | integer | Maximum occurrences for one end. Default is 100000. |
--max_hits_paired -n | integer | Maximum hits to output for paired reads. Default is 3. |
--max_hits_discordant -N | integer | Maximum hits to output for discordant pairs. Default is 10. |
--chimeric_rate -c | double | Prior of chimeric rate (lower bound). Default is 1.0e-05. |
Algorithm Options
Name | Type & Properties | Description |
|---|---|---|
--read_group -r | string | Read group header line such as '@RG\tID:foo\tSM:bar'. |
--preload_index -P | boolean_true | Preload index into memory (for base-space reads only). |
--disable_smith_waterman -s | boolean_true | Disable Smith-Waterman for the unmapped mate. |
--disable_insert_size_estimate -A | boolean_true | Disable insert size estimate (force -s). |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output.sam"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/biobox.git \
-revision v0.4.1 \
-main-script target/nextflow/bwa/bwa_sampe/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
bwa/bwa_sampebiobox v0.4.1
Uses
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