minibwa/minibwa_map

alignment

minibwa

BWA

BWA-MEM

mapping

Hi-C

bisulfite

long-read

Description

Align reads to a reference genome using minibwa, the successor to bwa-mem.
Combines BWA-MEM-style variable-length seeding with minimap2-style chaining
and SIMD alignment. Can handle short reads, long reads, Hi-C
proximity-ligation reads, and directional bisulfite (BS-seq) reads.

Input

Name	Type & Properties	Description
--index	file required	Directory containing the minibwa index files (`.l2b`, `.mbw`, and optionally `.meth.mbw`), as produced by `minibwa_index`.
--reads1	file required	Input FASTQ/FASTA file with first reads in pair (R1) or single-end/long reads.
--reads2	file	Input FASTQ file with second reads in pair (R2). Omit for single-end or long-read data.

Name

Type & Properties

--index

file

required

--reads1

file

required

--reads2

file

Output

Name	Type & Properties	Description
--output -o	file output	Output alignment file. In SAM format by default, or PAF format when `--paf_output` is set. If not specified, output goes to stdout.

Name

Type & Properties

--output

-o

file

output

Common Options

Name	Type & Properties	Description
--paf_output -f	boolean_true	Output in PAF format instead of SAM.
--short_read_threshold -l	integer	In the default adaptive mode, reads shorter than this length are treated as short reads. Default: 325.
--read_group -R	string	SAM read group line, e.g. `'@RG\tID:foo\tSM:bar'`.
--base_tag -b	string	Output a base alignment tag.
--hic	boolean_true	Map Hi-C proximity-ligation reads. Equivalent to setting `--primary_5prime` and `--skip_pairing`.
--meth	boolean_true	Map directional bisulfite sequencing (BS-seq) reads. Requires an index built with `minibwa_index --meth`.

Name

Type & Properties

--paf_output

-f

boolean_true

--short_read_threshold

-l

integer

--read_group

-R

string

--base_tag

-b

string

--hic

boolean_true

--meth

boolean_true

Mapping Options

Name	Type & Properties	Description
--min_seed_length -k	integer	Minimum seed length. Default: 19.
--max_seed_occurrences -c	integer	Maximum seed occurrences. Default: 250.
--max_gap_size -g	integer	Maximum gap size, controlling extension and chain breaking. Default: 100.
--bandwidth -w	integer	Bandwidth. Default: 100.
--long_bandwidth -W	integer	Long bandwidth, used for long reads or the adaptive mode. Default: 20000.
--min_chaining_score -m	integer	Minimum chaining score. Default: 25.
--secondary_ratio -p	double	Minimum secondary-to-primary score ratio. Default: 0.5.
--max_secondary -N	integer	Retain at most this many secondary alignments. Default: 50.
--chain_only	boolean_true	Perform chaining only, without base alignment.
--mode -x	string	Preset mode, which adaptively chooses parameters based on read length. Default: 'adap'.

Name

Type & Properties

--min_seed_length

-k

integer

--max_seed_occurrences

-c

integer

--max_gap_size

-g

integer

--bandwidth

-w

integer

--long_bandwidth

-W

integer

--min_chaining_score

-m

integer

--secondary_ratio

-p

double

--max_secondary

-N

integer

--chain_only

boolean_true

--mode

-x

string

Alignment Options

Name	Type & Properties	Description
--match_score -A	integer	Matching score. Default: 2.
--mismatch_penalty -B	integer	Mismatch penalty. Default: 8.
--gap_open_penalty -O	string	Gap open penalty for deletions and insertions. Default: '12,23'.
--gap_extend_penalty -E	string	Gap extension penalty. Default: '2,1'.
--min_score -s	integer	Suppress alignments with a DP score lower than `INT * match_score`. Default: 30.

Name

Type & Properties

--match_score

-A

integer

--mismatch_penalty

-B

integer

--gap_open_penalty

-O

string

--gap_extend_penalty

-E

string

--min_score

-s

integer

Paired-end Options

Name	Type & Properties	Description
--skip_pairing -P	boolean_true	Skip pairing and mate rescue.
--rescue	integer	Perform mate rescue for up to this many candidates. Set to 0 to skip rescue. Default: 10.

Name

Type & Properties

--skip_pairing

-P

boolean_true

--rescue

integer

Input/Output Options

Name	Type & Properties	Description
--no_unmapped -u	boolean_true	Don't output unmapped reads.
--secondary_output_limit --outn	integer	Output up to this many secondary alignments. Default: 0.
--xa_max_hits --xa	integer	If there are at most this many hits with a score above 80% of the best hit, output them all in the XA tag. Default: 5.
--copy_comments -y	boolean_true	Copy FASTA/FASTQ comments to the output.
--soft_clipping -Y	boolean_true	Use soft clipping for supplementary alignments.
--header -H	string	If the value starts with `@`, insert it into the header, otherwise treat it as a path to a file with lines to insert.
--primary_5prime -5	boolean_true	For split alignments, take the alignment with the smallest query position as primary.
--batch_size -K	string	Process NUM1-NUM2 bp of query sequences in a batch. Default: '100m,1g'.

Name

Type & Properties

--no_unmapped

-u

boolean_true

--secondary_output_limit

--outn

integer

--xa_max_hits

--xa

integer

--copy_comments

-y

boolean_true

--soft_clipping

-Y

boolean_true

--header

-H

string

--primary_5prime

-5

boolean_true

--batch_size

-K

string

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 v0.5.0 \  
  -main-script target/nextflow/minibwa/minibwa_map/main.nf \  
  -params-file params.yaml

minibwa/minibwa_map

Input

Output

Common Options

Mapping Options

Alignment Options

Paired-end Options

Input/Output Options

Run this component

Relationships

Used by

Uses