bwa/bwa_aln

alignment

BWA

BWA-aln

mapping

short-reads

Description

BWA aln algorithm for aligning short 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).
--reads	file required	Input FASTQ file with reads to align.

Name

Type & Properties

--index

file

required

--reads

file

required

Output

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

Name

Type & Properties

--output

-f

file

output

Algorithm Options

Name	Type & Properties	Description
--max_diff -n	string	Max #diff (int) or missing prob under 0.02 err rate (float). Default is 0.04.
--max_gap_opens -o	integer	Maximum number or fraction of gap opens. Default is 1.
--max_gap_extensions -e	integer	Maximum number of gap extensions, -1 for disabling long gaps. Default is -1.
--indel_end_skip -i	integer	Do not put an indel within INT bp towards the ends. Default is 5.
--max_long_deletion_extensions -d	integer	Maximum occurrences for extending a long deletion. Default is 10.
--seed_length -l	integer	Seed length. Default is 32.
--max_seed_diff -k	integer	Maximum differences in the seed. Default is 2.
--max_queue_entries -m	integer	Maximum entries in the queue. Default is 2000000.

Name

Type & Properties

--max_diff

-n

string

--max_gap_opens

-o

integer

--max_gap_extensions

-e

integer

--indel_end_skip

-i

integer

--max_long_deletion_extensions

-d

integer

--seed_length

-l

integer

--max_seed_diff

-k

integer

--max_queue_entries

-m

integer

Scoring Options

Name	Type & Properties	Description
--mismatch_penalty -M	integer	Mismatch penalty. Default is 3.
--gap_open_penalty -O	integer	Gap open penalty. Default is 11.
--gap_extension_penalty -E	integer	Gap extension penalty. Default is 4.
--stop_search_threshold -R	integer	Stop searching when there are >INT equally best hits. Default is 30.
--quality_threshold -q	integer	Quality threshold for read trimming down to 35bp. Default is 0.

Name

Type & Properties

--mismatch_penalty

-M

integer

--gap_open_penalty

-O

integer

--gap_extension_penalty

-E

integer

--stop_search_threshold

-R

integer

--quality_threshold

-q

integer

Input/Output Options

Name	Type & Properties	Description
--barcode_length -B	integer	Length of barcode.
--log_gap_penalty -L	boolean_true	Log-scaled gap penalty for long deletions.
--non_iterative -N	boolean_true	Non-iterative mode - search for all n-difference hits (slow).
--illumina_13_format -I	boolean_true	The input is in the Illumina 1.3+ FASTQ-like format.
--input_bam -b	boolean_true	The input read file is in the BAM format.
--single_end_only -0	boolean_true	Use single-end reads only (effective with -b).
--use_first_read -1	boolean_true	Use the 1st read in a pair (effective with -b).
--use_second_read -2	boolean_true	Use the 2nd read in a pair (effective with -b).
--filter_casava -Y	boolean_true	Filter Casava-filtered sequences.

Name

Type & Properties

--barcode_length

-B

integer

--log_gap_penalty

-L

boolean_true

--non_iterative

-N

boolean_true

--illumina_13_format

-I

boolean_true

--input_bam

-b

boolean_true

--single_end_only

-0

boolean_true

--use_first_read

-1

boolean_true

--use_second_read

-2

boolean_true

--filter_casava

-Y

boolean_true

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.sai"  
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_aln/main.nf \  
  -params-file params.yaml

bwa/bwa_aln

Input

Output

Algorithm Options

Scoring Options

Input/Output Options

Run this component

Relationships

Used by

Uses