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 a FASTA file <s> 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:

--ma <int>

match bonus (0 for --end-to-end, 2 for --local)

--mp <int>

max penalty for mismatch; lower qual = lower penalty (6)

--np <int>

penalty for non-A/C/G/Ts in read/ref (1)

--rdg <int>,<int>

read gap open, extend penalties (5,3)

--rfg <int>,<int>

reference gap open, extend penalties (5,3)

--score-min <func> min acceptable alignment score w/r/t read length

(G,20,8 for local, L,-0.6,-0.6 for end-to-end)

Reporting:

(default)

look for multiple alignments, report best, with MAPQ

OR

-k <int>

report up to <int> alns per read; MAPQ not meaningful

OR

-a/--all

report all alignments; very slow, MAPQ not meaningful

Effort:

-D <int>

give up extending after <int> failed extends in a row (15)

-R <int>

for reads w/ repetitive seeds, try <int> sets of seeds (2)

Paired-end:

-I/--minins <int>

minimum fragment length (0)

-X/--maxins <int>

maximum fragment length (500)

--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

--un <path>

write unpaired reads that didn't align to <path>

--al <path>

write unpaired reads that aligned at least once to <path>

--un-conc <path>

write pairs that didn't align concordantly to <path>

--al-conc <path>

write pairs that aligned concordantly at least once to <path>

(Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g. --un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)

--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

Performance:

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

--reorder

force SAM output order to match order of input reads

--mm

use memory-mapped I/O for index; many 'bowtie's can share

Other:

--qc-filter

filter out reads that are bad according to QSEQ filter

--seed <int>

seed for random number generator (0)

--non-deterministic

seed rand. gen. arbitrarily instead of using read attributes

--version

print version information and quit

-h/--help

print this usage message