bowtie2/bowtie2_align

Alignment

Sequencing

Description

Align single-end and paired-end reads to a reference genome using Bowtie2.

Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads
to long reference sequences. It is particularly good at aligning reads of about
50 up to 100s of characters, and particularly good at aligning to relatively
long (e.g. mammalian) genomes.

Inputs

Name	Type & Properties	Description
--index	string required	Index filename prefix (minus trailing .X.bt2).
--mate1	file multiple	Files with #1 mates, paired with files in --mate2.
--mate2	file multiple	Files with #2 mates, paired with files in --mate1.
--unpaired	file multiple	Files with unpaired reads.
--interleaved	file multiple	Files with interleaved paired-end FASTQ/FASTA reads.
--bam_input	file multiple	Files are unaligned BAM sorted by read name.

Name

Type & Properties

--index

string

required

--mate1

file

multiple

--mate2

file

multiple

--unpaired

file

multiple

--interleaved

file

multiple

--bam_input

file

multiple

Outputs

Name	Type & Properties	Description
--output	file required output	File for SAM output (default stdout).
--un	file output	Write unpaired reads that didn't align to file.
--al	file output	Write unpaired reads that aligned at least once to file.
--un_conc	file output	Write pairs that didn't align concordantly to file.
--al_conc	file output	Write pairs that aligned concordantly at least once to file.
--met_file	file output	Send metrics to file.

Name

Type & Properties

--output

file

required

output

--un

file

output

--al

file

output

--un_conc

file

output

--al_conc

file

output

--met_file

file

output

Input Format Options

Name	Type & Properties	Description
--fastq	boolean_true	Query input files are FASTQ .fq/.fastq (default).
--tab5	boolean_true	Query input files are TAB5 .tab5.
--tab6	boolean_true	Query input files are TAB6 .tab6.
--qseq	boolean_true	Query input files are in Illumina's qseq format.
--fasta	boolean_true	Query input files are (multi-)FASTA .fa/.mfa.
--raw	boolean_true	Query input files are raw one-sequence-per-line.
--cmdline	boolean_true	<m1>, <m2>, <r> are sequences themselves, not files.
--skip	integer	Skip the first <int> reads/pairs in the input.
--upto	integer	Stop after first <int> reads/pairs.
--trim5	integer	Trim <int> bases from 5'/left end of reads.
--trim3	integer	Trim <int> bases from 3'/right end of reads.
--trim_to	string	Trim reads exceeding <int> bases from either 3' or 5' end. Format: [3:\|5:]<int>
--continuous_fasta	string	Query input files are continuous FASTA where reads are k-mers. Format: k:<int>,i:<int>
--phred33	boolean_true	Qualities are Phred+33 (default).
--phred64	boolean_true	Qualities are Phred+64.
--int_quals	boolean_true	Qualities encoded as space-delimited integers.

Name

Type & Properties

--fastq

boolean_true

--tab5

boolean_true

--tab6

boolean_true

--qseq

boolean_true

--fasta

boolean_true

--raw

boolean_true

--cmdline

boolean_true

--skip

integer

--upto

integer

--trim5

integer

--trim3

integer

--trim_to

string

--continuous_fasta

string

--phred33

boolean_true

--phred64

boolean_true

--int_quals

boolean_true

Alignment Presets

Name	Type & Properties	Description
--very_fast	boolean_true	Same as -D 5 -R 1 -N 0 -L 22 -i S,0,2.50.
--fast	boolean_true	Same as -D 10 -R 2 -N 0 -L 22 -i S,0,2.50.
--sensitive	boolean_true	Same as -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default).
--very_sensitive	boolean_true	Same as -D 20 -R 3 -N 0 -L 20 -i S,1,0.50.
--very_fast_local	boolean_true	Same as -D 5 -R 1 -N 0 -L 25 -i S,1,2.00.
--fast_local	boolean_true	Same as -D 10 -R 2 -N 0 -L 22 -i S,1,1.75.
--sensitive_local	boolean_true	Same as -D 15 -R 2 -N 0 -L 20 -i S,1,0.75.
--very_sensitive_local	boolean_true	Same as -D 20 -R 3 -N 0 -L 20 -i S,1,0.50.

Name

Type & Properties

--very_fast

boolean_true

--fast

boolean_true

--sensitive

boolean_true

--very_sensitive

boolean_true

--very_fast_local

boolean_true

--fast_local

boolean_true

--sensitive_local

boolean_true

--very_sensitive_local

boolean_true

Alignment Options

Name	Type & Properties	Description
--N	integer	Max # mismatches in seed alignment; can be 0 or 1.
--L	integer	Length of seed substrings; must be >3, <32.
--i	string	Interval between seed substrings w/r/t read len.
--n_ceil	string	Function for max # non-A/C/G/Ts permitted in aln.
--dpad	integer	Include <int> extra ref chars on sides of DP table.
--gbar	integer	Disallow gaps within <int> nucs of read extremes.
--ignore_quals	boolean_true	Treat all quality values as 30 on Phred scale.
--nofw	boolean_true	Do not align forward (original) version of read.
--norc	boolean_true	Do not align reverse-complement version of read.
--no_1mm_upfront	boolean_true	Do not allow 1 mismatch alignments before attempting to scan for the optimal seeded alignments.
--end_to_end	boolean_true	Entire read must align; no clipping (default).
--local	boolean_true	Local alignment; ends might be soft clipped.

Name

Type & Properties

--N

integer

--L

integer

--i

string

--n_ceil

string

--dpad

integer

--gbar

integer

--ignore_quals

boolean_true

--nofw

boolean_true

--norc

boolean_true

--no_1mm_upfront

boolean_true

--end_to_end

boolean_true

--local

boolean_true

Scoring Options

Name	Type & Properties	Description
--ma	integer	Match bonus (0 for --end-to-end, 2 for --local).
--mp	string	Max penalty for mismatch; lower qual = lower penalty.
--np	integer	Penalty for non-A/C/G/Ts in read/ref.
--rdg	string	Read gap open, extend penalties.
--rfg	string	Reference gap open, extend penalties.
--score_min	string	Min acceptable alignment score w/r/t read length.

Name

Type & Properties

--ma

integer

--mp

string

--np

integer

--rdg

string

--rfg

string

--score_min

string

Reporting Options

Name	Type & Properties	Description
--k	integer	Report up to <int> alns per read; MAPQ not meaningful.
--all	boolean_true	Report all alignments; very slow, MAPQ not meaningful.

Name

Type & Properties

--k

integer

--all

boolean_true

Effort Options

Name	Type & Properties	Description
--D	integer	Give up extending after <int> failed extends in a row.
--R	integer	For reads w/ repetitive seeds, try <int> sets of seeds.

Name

Type & Properties

--D

integer

--R

integer

Paired-end Options

Name	Type & Properties	Description
--minins	integer	Minimum fragment length.
--maxins	integer	Maximum fragment length.
--fr	boolean_true	-1, -2 mates align fw/rev (default).
--rf	boolean_true	-1, -2 mates align rev/fw.
--ff	boolean_true	-1, -2 mates align fw/fw.
--no_mixed	boolean_true	Suppress unpaired alignments for paired reads.
--no_discordant	boolean_true	Suppress discordant alignments for paired reads.
--dovetail	boolean_true	Concordant when mates extend past each other.
--no_contain	boolean_true	Not concordant when one mate alignment contains other.
--no_overlap	boolean_true	Not concordant when mates overlap at all.

Name

Type & Properties

--minins

integer

--maxins

integer

--fr

boolean_true

--rf

boolean_true

--ff

boolean_true

--no_mixed

boolean_true

--no_discordant

boolean_true

--dovetail

boolean_true

--no_contain

boolean_true

--no_overlap

boolean_true

SAM Output Options

Name	Type & Properties	Description
--time	boolean_true	Print wall-clock time taken by search phases.
--quiet	boolean_true	Print nothing to stderr except serious errors.
--met_stderr	boolean_true	Send metrics to stderr.
--met	integer	Report internal counters & metrics every <int> secs.
--no_unal	boolean_true	Suppress SAM records for unaligned reads.
--no_head	boolean_true	Suppress header lines, i.e. lines starting with @.
--no_sq	boolean_true	Suppress @SQ header lines.
--rg_id	string	Set read group id, reflected in @RG line and RG:Z: opt field.
--rg	string	Add <text> ("lab:value") to @RG line of SAM header.
--omit_sec_seq	boolean_true	Put '*' in SEQ and QUAL fields for secondary alignments.
--sam_no_qname_trunc	boolean_true	Suppress standard behavior of truncating readname at first whitespace.
--xeq	boolean_true	Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.
--soft_clipped_unmapped_tlen	boolean_true	Exclude soft-clipped bases when reporting TLEN.
--sam_append_comment	boolean_true	Append FASTA/FASTQ comment to SAM record.
--sam_opt_config	string	Use config to toggle SAM Optional fields. Example: '-MD,YP,-AS'

Name

Type & Properties

--time

boolean_true

--quiet

boolean_true

--met_stderr

boolean_true

--met

integer

--no_unal

boolean_true

--no_head

boolean_true

--no_sq

boolean_true

--rg_id

string

--rg

string

--omit_sec_seq

boolean_true

--sam_no_qname_trunc

boolean_true

--xeq

boolean_true

--soft_clipped_unmapped_tlen

boolean_true

--sam_append_comment

boolean_true

--sam_opt_config

string

BAM Options

Name	Type & Properties	Description
--align_paired_reads	boolean_true	Align paired-end reads instead of unpaired BAM reads.
--preserve_tags	boolean_true	Preserve tags from the original BAM record.

Name

Type & Properties

--align_paired_reads

boolean_true

--preserve_tags

boolean_true

Performance Options

Name	Type & Properties	Description
--reorder	boolean_true	Force SAM output order to match order of input reads.
--mm	boolean_true	Use memory-mapped I/O for index; many 'bowtie's can share.

Name

Type & Properties

--reorder

boolean_true

--mm

boolean_true

Other Options

Name	Type & Properties	Description
--qc_filter	boolean_true	Filter out reads that are bad according to QSEQ filter.
--seed	integer	Seed for random number generator.
--non_deterministic	boolean_true	Seed rand. gen. arbitrarily instead of using read attributes.

Name

Type & Properties

--qc_filter

boolean_true

--seed

integer

--non_deterministic

boolean_true

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.sam"  
un: "$id.$key.un.fastq"  
al: "$id.$key.al.fastq"  
un_conc: "$id.$key.un_conc.fastq"  
al_conc: "$id.$key.al_conc.fastq"  
met_file: "$id.$key.met_file.txt"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.0 \  
  -main-script target/nextflow/bowtie2/bowtie2_align/main.nf \  
  -params-file params.yaml

bowtie2/bowtie2_align

Inputs

Outputs

Input Format Options

Alignment Presets

Alignment Options

Scoring Options

Reporting Options

Effort Options

Paired-end Options

SAM Output Options

BAM Options

Performance Options

Other Options

Run this component

Relationships

Used by

Uses