bowtie2-align-l1

Input:

-q

query input files are FASTQ .fq/.fastq (default)

--tab5

query input files are TAB5 .tab5

--tab6

query input files are TAB6 .tab6

--qseq

query input files are in Illumina's qseq format

-f

query input files are (multi-)FASTA .fa/.mfa

-r

query input files are raw one-sequence-per-line

-F k:<int>,i:<int> query input files are continuous FASTA where reads

are substrings (k-mers) extracted from the FASTA file and aligned at offsets 1, 1+i, 1+2i ... end of reference

-c

<m1>, <m2>, <r> are sequences themselves, not files

-s/--skip <int>

skip the first <int> reads/pairs in the input (none)

-u/--upto <int>

stop after first <int> reads/pairs (no limit)

-5/--trim5 <int>

trim <int> bases from 5'/left end of reads (0)

-3/--trim3 <int>

trim <int> bases from 3'/right end of reads (0)

--trim-to [3:|5:]<int> trim reads exceeding <int> bases from either 3' or 5' end

If the read end is not specified then it defaults to 3 (0)

--phred33

qualities are Phred+33 (default)

--phred64

qualities are Phred+64

--int-quals

qualities encoded as space-delimited integers

Presets:

Same as:

For --end-to-end:

--very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50

--fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50

--sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)

--very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

For --local:

--very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00

--fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75

--sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)

--very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

Alignment:

-N <int>

max # mismatches in seed alignment; can be 0 or 1 (0)

-L <int>

length of seed substrings; must be >3, <32 (22)

-i <func>

interval between seed substrings w/r/t read len (S,1,1.15)

--n-ceil <func>

func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)

--dpad <int>

include <int> extra ref chars on sides of DP table (15)

--gbar <int>

disallow gaps within <int> nucs of read extremes (4)

--ignore-quals

treat all quality values as 30 on Phred scale (off)

--nofw

do not align forward (original) version of read (off)

--norc

do not align reverse-complement version of read (off)

--no-1mm-upfront

do not allow 1 mismatch alignments before attempting to scan for the optimal seeded alignments

--end-to-end

entire read must align; no clipping (on)

OR

--local

local alignment; ends might be soft clipped (off)

Scoring:

Reporting:

Effort:

--fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)

--no-mixed

suppress unpaired alignments for paired reads

--no-discordant

suppress discordant alignments for paired reads

--dovetail

concordant when mates extend past each other

--no-contain

not concordant when one mate alignment contains other

--no-overlap

not concordant when mates overlap at all

BAM:

--align-paired-reads

Bowtie2 will, by default, attempt to align unpaired BAM reads. Use this option to align paired-end reads instead.

--preserve-tags

Preserve tags from the original BAM record by appending them to the end of the corresponding SAM output.

Output:

-t/--time

print wall-clock time taken by search phases

--quiet

print nothing to stderr except serious errors

--met-file <path>

send metrics to file at <path> (off)

--met-stderr

send metrics to stderr (off)

--met <int>

report internal counters & metrics every <int> secs (1)

--no-unal

suppress SAM records for unaligned reads

--no-head

suppress header lines, i.e. lines starting with @

--no-sq

suppress @SQ header lines

--rg-id <text>

set read group id, reflected in @RG line and RG:Z: opt field

--rg <text>

add <text> ("lab:value") to @RG line of SAM header. Note: @RG line only printed when --rg-id is set.

--omit-sec-seq

put '*' in SEQ and QUAL fields for secondary alignments.

--sam-no-qname-trunc

Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM.

--xeq

Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.

--soft-clipped-unmapped-tlen

Exclude soft-clipped bases when reporting TLEN.

--sam-append-comment

Append FASTA/FASTQ comment to SAM record.

--sam-opt-config <config>

Use <config>, example '-MD,YP,-AS', to toggle SAM Optional fields.

Performance:

-p/--threads <int> number of alignment threads to launch (1)

Other: