bwa/bwa_mem

alignment

BWA

BWA-MEM

mapping

Description

BWA-MEM algorithm for aligning sequence reads to a reference genome.

Input

Name	Type & Properties	Description
--index	file required	BWA index base name (prefix of .amb, .ann, .bwt, .pac, .sa files).
--reads1	file required	Input FASTQ file with first reads in pair (R1) or single-end reads.
--reads2	file	Input FASTQ file with second reads in pair (R2). Optional for single-end.

Name

Type & Properties

--index

file

required

--reads1

file

required

--reads2

file

Output

Name	Type & Properties	Description
--output -o	file output	Output SAM file. If not specified, output goes to stdout.

Name

Type & Properties

--output

-o

file

output

Algorithm Options

Name	Type & Properties	Description
--min_seed_length -k	integer	Minimum seed length. Default is 19.
--band_width -w	integer	Band width for banded alignment. Default is 100.
--dropoff -d	integer	Off-diagonal X-dropoff. Default is 100.
--reseed_ratio -r	double	Look for internal seeds inside a seed longer than {-k} * FLOAT. Default is 1.5.
--seed_occurrence -y	integer	Seed occurrence for the 3rd round seeding. Default is 20.
--skip_seeds -c	integer	Skip seeds with more than INT occurrences. Default is 500.
--chain_drop -D	double	Drop chains shorter than FLOAT fraction of the longest overlapping chain. Default is 0.50.
--seeded_bases -W	integer	Discard a chain if seeded bases shorter than INT. Default is 0.
--mate_rescue -m	integer	Perform at most INT rounds of mate rescues for each read. Default is 50.
--skip_mate_rescue -S	boolean_true	Skip mate rescue.
--skip_pairing -P	boolean_true	Skip pairing; mate rescue performed unless -S also in use.

Name

Type & Properties

--min_seed_length

-k

integer

--band_width

-w

integer

--dropoff

-d

integer

--reseed_ratio

-r

double

--seed_occurrence

-y

integer

--skip_seeds

-c

integer

--chain_drop

-D

double

--seeded_bases

-W

integer

--mate_rescue

-m

integer

--skip_mate_rescue

-S

boolean_true

--skip_pairing

-P

boolean_true

Scoring Options

Name	Type & Properties	Description
--match_score -A	integer	Score for a sequence match. Default is 1.
--mismatch_penalty -B	integer	Penalty for a mismatch. Default is 4.
--gap_open_penalty -O	string	Gap open penalties for deletions and insertions. Default is 6,6.
--gap_extend_penalty -E	string	Gap extension penalty. Default is 1,1.
--clipping_penalty -L	string	Penalty for 5'- and 3'-end clipping. Default is 5,5.
--unpaired_penalty -U	integer	Penalty for an unpaired read pair. Default is 17.
--read_type -x	string	Read type preset (pacbio, ont2d, intractg).

Name

Type & Properties

--match_score

-A

integer

--mismatch_penalty

-B

integer

--gap_open_penalty

-O

string

--gap_extend_penalty

-E

string

--clipping_penalty

-L

string

--unpaired_penalty

-U

integer

--read_type

-x

string

Input/Output Options

Name	Type & Properties	Description
--smart_pairing -p	boolean_true	Smart pairing (ignoring in2.fq).
--read_group -R	string	Read group header line such as '@RG\tID:foo\tSM:bar'.
--header -H	string	Insert STR to header if it starts with @; or insert lines in FILE.
--ignore_alt -j	boolean_true	Treat ALT contigs as part of the primary assembly.
--primary_5prime -5	boolean_true	For split alignment, take the alignment with the smallest query (not genomic) coordinate as primary.
--keep_mapq -q	boolean_true	Don't modify mapQ of supplementary alignments.
--batch_size -K	integer	Process INT input bases in each batch regardless of nThreads.
--verbosity -v	integer	Verbosity level (1=error, 2=warning, 3=message, 4+=debugging). Default is 3.
--min_score -T	integer	Minimum score to output. Default is 30.
--max_hits_xa	string	If there are <INT hits with score >80.00% of the max score, output all in XA. Default is 5,200.
--score_fraction -z	double	The fraction of the max score to use with -h. Default is 0.800000.
--output_all -a	boolean_true	Output all alignments for SE or unpaired PE.
--append_comment -C	boolean_true	Append FASTA/FASTQ comment to SAM output.
--output_ref_header -V	boolean_true	Output the reference FASTA header in the XR tag.
--soft_clipping -Y	boolean_true	Use soft clipping for supplementary alignments.
--mark_secondary -M	boolean_true	Mark shorter split hits as secondary.
--output_xb -u	boolean_true	Output XB instead of XA; XB is XA with the alignment score and mapping quality added.
--insert_size -I	string	Specify the mean, standard deviation, max and min of the insert size distribution.

Name

Type & Properties

--smart_pairing

-p

boolean_true

--read_group

-R

string

--header

-H

string

--ignore_alt

-j

boolean_true

--primary_5prime

-5

boolean_true

--keep_mapq

-q

boolean_true

--batch_size

-K

integer

--verbosity

-v

integer

--min_score

-T

integer

--max_hits_xa

string

--score_fraction

-z

double

--output_all

-a

boolean_true

--append_comment

-C

boolean_true

--output_ref_header

-V

boolean_true

--soft_clipping

-Y

boolean_true

--mark_secondary

-M

boolean_true

--output_xb

-u

boolean_true

--insert_size

-I

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 v0.4.2 \  
  -main-script target/nextflow/bwa/bwa_mem/main.nf \  
  -params-file params.yaml

bwa/bwa_mem

Input

Output

Algorithm Options

Scoring Options

Input/Output Options

Run this component

Relationships

Used by

Uses