.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.48.2.
.TH BOWTIE2 "1" "March 2021" "bowtie2 2.4.2" "User Commands"
.SH NAME
bowtie2 \- wrapper for bowtie2-align-*
.SH DESCRIPTION

Bowtie 2 version 2.4.2 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
.SH
USAGE
bowtie2 [options]* \fB\-x\fR <bt2\-idx> {\-1 <m1> \fB\-2\fR <m2> | \fB\-U\fR <r> | \fB\-\-interleaved\fR <i> | \fB\-b\fR <bam>} [\-S <sam>]
.TP
<bt2\-idx>
Index filename prefix (minus trailing .X.bt2).
NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
.TP
<m1>
Files with #1 mates, paired with files in <m2>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
.TP
<m2>
Files with #2 mates, paired with files in <m1>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
.TP
<r>
Files with unpaired reads.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
.TP
<i>
Files with interleaved paired\-end FASTQ/FASTA reads
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
.TP
<bam>
Files are unaligned BAM sorted by read name.
.TP
<sam>
File for SAM output (default: stdout)
.IP
<m1>, <m2>, <r> can be comma\-separated lists (no whitespace) and can be
specified many times.  E.g. '\-U file1.fq,file2.fq \fB\-U\fR file3.fq'.
.PP
.SH OPTIONS (defaults in parentheses)
.SS Input:
.TP
\fB\-q\fR
query input files are FASTQ .fq/.fastq (default)
.TP
\fB\-\-tab5\fR
query input files are TAB5 .tab5
.TP
\fB\-\-tab6\fR
query input files are TAB6 .tab6
.TP
\fB\-\-qseq\fR
query input files are in Illumina's qseq format
.TP
\fB\-f\fR
query input files are (multi\-)FASTA .fa/.mfa
.TP
\fB\-r\fR
query input files are raw one\-sequence\-per\-line
.TP
\fB\-F\fR 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
.TP
\fB\-c\fR
<m1>, <m2>, <r> are sequences themselves, not files
.TP
\fB\-s\fR/\-\-skip <int>
skip the first <int> reads/pairs in the input (none)
.TP
\fB\-u\fR/\-\-upto <int>
stop after first <int> reads/pairs (no limit)
.TP
\fB\-5\fR/\-\-trim5 <int>
trim <int> bases from 5'/left end of reads (0)
.TP
\fB\-3\fR/\-\-trim3 <int>
trim <int> bases from 3'/right end of reads (0)
.TP
\fB\-\-trim\-to\fR [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)
.TP
\fB\-\-phred33\fR
qualities are Phred+33 (default)
.TP
\fB\-\-phred64\fR
qualities are Phred+64
.TP
\fB\-\-int\-quals\fR
qualities encoded as space\-delimited integers
.SS Presets:
Same as:
.IP
For \fB\-\-end\-to\-end\fR:
.HP
\fB\-\-very\-fast\fR            \fB\-D\fR 5 \fB\-R\fR 1 \fB\-N\fR 0 \fB\-L\fR 22 \fB\-i\fR S,0,2.50
.HP
\fB\-\-fast\fR                 \fB\-D\fR 10 \fB\-R\fR 2 \fB\-N\fR 0 \fB\-L\fR 22 \fB\-i\fR S,0,2.50
.HP
\fB\-\-sensitive\fR            \fB\-D\fR 15 \fB\-R\fR 2 \fB\-N\fR 0 \fB\-L\fR 22 \fB\-i\fR S,1,1.15 (default)
.HP
\fB\-\-very\-sensitive\fR       \fB\-D\fR 20 \fB\-R\fR 3 \fB\-N\fR 0 \fB\-L\fR 20 \fB\-i\fR S,1,0.50
.IP
For \fB\-\-local\fR:
.HP
\fB\-\-very\-fast\-local\fR      \fB\-D\fR 5 \fB\-R\fR 1 \fB\-N\fR 0 \fB\-L\fR 25 \fB\-i\fR S,1,2.00
.HP
\fB\-\-fast\-local\fR           \fB\-D\fR 10 \fB\-R\fR 2 \fB\-N\fR 0 \fB\-L\fR 22 \fB\-i\fR S,1,1.75
.HP
\fB\-\-sensitive\-local\fR      \fB\-D\fR 15 \fB\-R\fR 2 \fB\-N\fR 0 \fB\-L\fR 20 \fB\-i\fR S,1,0.75 (default)
.HP
\fB\-\-very\-sensitive\-local\fR \fB\-D\fR 20 \fB\-R\fR 3 \fB\-N\fR 0 \fB\-L\fR 20 \fB\-i\fR S,1,0.50
.SS Alignment:
.TP
\fB\-N\fR <int>
max # mismatches in seed alignment; can be 0 or 1 (0)
.TP
\fB\-L\fR <int>
length of seed substrings; must be >3, <32 (22)
.TP
\fB\-i\fR <func>
interval between seed substrings w/r/t read len (S,1,1.15)
.TP
\fB\-\-n\-ceil\fR <func>
func for max # non\-A/C/G/Ts permitted in aln (L,0,0.15)
.TP
\fB\-\-dpad\fR <int>
include <int> extra ref chars on sides of DP table (15)
.TP
\fB\-\-gbar\fR <int>
disallow gaps within <int> nucs of read extremes (4)
.TP
\fB\-\-ignore\-quals\fR
treat all quality values as 30 on Phred scale (off)
.TP
\fB\-\-nofw\fR
do not align forward (original) version of read (off)
.TP
\fB\-\-norc\fR
do not align reverse\-complement version of read (off)
.TP
\fB\-\-no\-1mm\-upfront\fR
do not allow 1 mismatch alignments before attempting to
scan for the optimal seeded alignments
.TP
\fB\-\-end\-to\-end\fR
entire read must align; no clipping (on)
.IP
OR
.TP
\fB\-\-local\fR
local alignment; ends might be soft clipped (off)
.SS Scoring:
.TP
\fB\-\-ma\fR <int>
match bonus (0 for \fB\-\-end\-to\-end\fR, 2 for \fB\-\-local\fR)
.TP
\fB\-\-mp\fR <int>
max penalty for mismatch; lower qual = lower penalty (6)
.TP
\fB\-\-np\fR <int>
penalty for non\-A/C/G/Ts in read/ref (1)
.TP
\fB\-\-rdg\fR <int>,<int>
read gap open, extend penalties (5,3)
.TP
\fB\-\-rfg\fR <int>,<int>
reference gap open, extend penalties (5,3)
.TP
\fB\-\-score\-min\fR <func> min acceptable alignment score w/r/t read length
(G,20,8 for local, L,\-0.6,\-0.6 for end\-to\-end)
.SS Reporting:
.TP
(default)
look for multiple alignments, report best, with MAPQ
.IP
OR
.TP
\fB\-k\fR <int>
report up to <int> alns per read; MAPQ not meaningful
.IP
OR
.TP
\fB\-a\fR/\-\-all
report all alignments; very slow, MAPQ not meaningful
.SS Effort:
.TP
\fB\-D\fR <int>
give up extending after <int> failed extends in a row (15)
.TP
\fB\-R\fR <int>
for reads w/ repetitive seeds, try <int> sets of seeds (2)
.IP
Paired\-end:
.TP
\fB\-I\fR/\-\-minins <int>
minimum fragment length (0)
.TP
\fB\-X\fR/\-\-maxins <int>
maximum fragment length (500)
.HP
\fB\-\-fr\fR/\-\-rf/\-\-ff     \fB\-1\fR, \fB\-2\fR mates align fw/rev, rev/fw, fw/fw (\fB\-\-fr\fR)
.TP
\fB\-\-no\-mixed\fR
suppress unpaired alignments for paired reads
.TP
\fB\-\-no\-discordant\fR
suppress discordant alignments for paired reads
.TP
\fB\-\-dovetail\fR
concordant when mates extend past each other
.TP
\fB\-\-no\-contain\fR
not concordant when one mate alignment contains other
.TP
\fB\-\-no\-overlap\fR
not concordant when mates overlap at all
.IP
BAM:
.TP
\fB\-\-align\-paired\-reads\fR
Bowtie2 will, by default, attempt to align unpaired BAM reads.
Use this option to align paired\-end reads instead.
.TP
\fB\-\-preserve\-tags\fR
Preserve tags from the original BAM record by
appending them to the end of the corresponding SAM output.
.SS Output:
.TP
\fB\-t\fR/\-\-time
print wall\-clock time taken by search phases
.TP
\fB\-\-un\fR <path>
write unpaired reads that didn't align to <path>
.TP
\fB\-\-al\fR <path>
write unpaired reads that aligned at least once to <path>
.TP
\fB\-\-un\-conc\fR <path>
write pairs that didn't align concordantly to <path>
.TP
\fB\-\-al\-conc\fR <path>
write pairs that aligned concordantly at least once to <path>
.IP
(Note: for \fB\-\-un\fR, \fB\-\-al\fR, \fB\-\-un\-conc\fR, or \fB\-\-al\-conc\fR, add '\-gz' to the option name, e.g.
\fB\-\-un\-gz\fR <path>, to gzip compress output, or add '\-bz2' to bzip2 compress output.)
.TP
\fB\-\-quiet\fR
print nothing to stderr except serious errors
.TP
\fB\-\-met\-file\fR <path>
send metrics to file at <path> (off)
.TP
\fB\-\-met\-stderr\fR
send metrics to stderr (off)
.TP
\fB\-\-met\fR <int>
report internal counters & metrics every <int> secs (1)
.TP
\fB\-\-no\-unal\fR
suppress SAM records for unaligned reads
.TP
\fB\-\-no\-head\fR
suppress header lines, i.e. lines starting with @
.TP
\fB\-\-no\-sq\fR
suppress @SQ header lines
.TP
\fB\-\-rg\-id\fR <text>
set read group id, reflected in @RG line and RG:Z: opt field
.TP
\fB\-\-rg\fR <text>
add <text> ("lab:value") to @RG line of SAM header.
Note: @RG line only printed when \fB\-\-rg\-id\fR is set.
.TP
\fB\-\-omit\-sec\-seq\fR
put '*' in SEQ and QUAL fields for secondary alignments.
.TP
\fB\-\-sam\-no\-qname\-trunc\fR
Suppress standard behavior of truncating readname at first whitespace
at the expense of generating non\-standard SAM.
.TP
\fB\-\-xeq\fR
Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.
.TP
\fB\-\-soft\-clipped\-unmapped\-tlen\fR
Exclude soft\-clipped bases when reporting TLEN
.TP
\fB\-\-sam\-append\-comment\fR
Append FASTA/FASTQ comment to SAM record
.SS Performance:
.HP
\fB\-p\fR/\-\-threads <int> number of alignment threads to launch (1)
.TP
\fB\-\-reorder\fR
force SAM output order to match order of input reads
.TP
\fB\-\-mm\fR
use memory\-mapped I/O for index; many 'bowtie's can share
.SS Other:
.TP
\fB\-\-qc\-filter\fR
filter out reads that are bad according to QSEQ filter
.TP
\fB\-\-seed\fR <int>
seed for random number generator (0)
.TP
\fB\-\-non\-deterministic\fR
seed rand. gen. arbitrarily instead of using read attributes
.TP
\fB\-\-version\fR
print version information and quit
.TP
\fB\-h\fR/\-\-help
print this usage message
.PP