BOWTIE2(1)

📦

version 2.5.5 · 9 versions

✨ NAME ✨

bowtie2 — literally just a wrapper for bowtie2-align-*, bestie 💅

🦋 DESCRIPTION 🦋

Okay so. Bowtie 2 version 2.5.5, made by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea). Iconic. Periodt. 👑

🌸 USAGE 🌸

bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> |
--interleaved <i> | -b <bam>} [-S <sam>]

Here's the whole cast of characters, no cap:

<bt2-idx> — the index filename prefix (minus the trailing .X.bt2). ⚠️ NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible, so don't even try it, they're not the same girlies.
<m1> — files with the #1 mates, paired with whatever's in <m2>. Can be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<m2> — files with the #2 mates, paired with whatever's in <m1>. Also can be gzip'ed (.gz) or bzip2'ed (.bz2).
<r> — files with unpaired reads. You guessed it: gzip'ed (.gz) or bzip2'ed (.bz2) is fine. 🫶
<i> — files with interleaved paired-end FASTQ/FASTA reads. Could be gzip'ed (.gz) or bzip2'ed (.bz2), obviously. ✨
<bam> — files are unaligned BAM sorted by read name.
<sam> — the file for SAM output (default: stdout).

Also, <m1>, <m2> and <r> can be comma-separated lists (no whitespace!! like, zero) and you can specify them many times. E.g. '-U file1.fq,file2.fq -U file3.fq'. 🌈

👑 OPTIONS 👑

(defaults are in parentheses, so you always know what you're getting)

💖 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)

--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

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

-a/--all — report all alignments; very slow without -l, MAPQ not meaningful

🔥 Effort

-l/--lowseeds <n> — ignore any low quality seeds with ranges over threshold (0=no cut, if percentage, mili or nano, relative to idx size)
-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)
-d/--deterministic-seeds — Consider all seeds in order (no subsampling, best with -a)

🫶 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, bestie: 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.
--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)
--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

That's the whole thing, and honestly? Ate. 💅

So this little love letter to your terminal is bowtie2 2.5.5, dated February 2026, and it lives in the BOWTIE2(1) section of your manual. Go forth and align, bestie 🫶✨🧬

📦 where this page comes from

ubuntu stonking: bowtie2 2.5.5-1 · GPL-3.0-or-later
💖 girlified by deepseek-ai/DeepSeek-V4.1-Flash on 2026-11-02: a language model's rewrite of the original, under its terms