1BOWTIE2(1)                       User Commands                      BOWTIE2(1)
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NAME

6       bowtie2 - manual page for bowtie2 2.4.1
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DESCRIPTION

9       Bowtie   2   version   2.4.1   by   Ben  Langmead  (langmea@cs.jhu.edu,
10       www.cs.jhu.edu/~langmea) Usage:
11
12              bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2  <m2>  |  -U  <r>  |
13              --interleaved <i> | -b <bam>} [-S <sam>]
14
15       <bt2-idx>
16              Index  filename  prefix (minus trailing .X.bt2).  NOTE: Bowtie 1
17              and Bowtie 2 indexes are not compatible.
18
19       <m1>   Files with #1 mates,  paired  with  files  in  <m2>.   Could  be
20              gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
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22       <m2>   Files  with  #2  mates,  paired  with  files  in <m1>.  Could be
23              gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
24
25       <r>    Files with unpaired reads.  Could be gzip'ed (extension: .gz) or
26              bzip2'ed (extension: .bz2).
27
28       <i>    Files  with  interleaved  paired-end  FASTQ/FASTA reads Could be
29              gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
30
31       <bam>  Files are unaligned BAM sorted by read name.
32
33       <sam>  File for SAM output (default: stdout)
34
35              <m1>, <m2>, <r> can be comma-separated lists (no whitespace) and
36              can  be  specified  many  times.   E.g. '-U file1.fq,file2.fq -U
37              file3.fq'.
38
39       Options (defaults in parentheses):
40
41              Input:
42
43       -q     query input files are FASTQ .fq/.fastq (default)
44
45       --tab5 query input files are TAB5 .tab5
46
47       --tab6 query input files are TAB6 .tab6
48
49       --qseq query input files are in Illumina's qseq format
50
51       -f     query input files are (multi-)FASTA .fa/.mfa
52
53       -r     query input files are raw one-sequence-per-line
54
55       -F k:<int>,i:<int> query input files are continuous FASTA where reads
56              are substrings (k-mers) extracted from  a  FASTA  file  <s>  and
57              aligned at offsets 1, 1+i, 1+2i ... end of reference
58
59       -c     <m1>, <m2>, <r> are sequences themselves, not files
60
61       -s/--skip <int>
62              skip the first <int> reads/pairs in the input (none)
63
64       -u/--upto <int>
65              stop after first <int> reads/pairs (no limit)
66
67       -5/--trim5 <int>
68              trim <int> bases from 5'/left end of reads (0)
69
70       -3/--trim3 <int>
71              trim <int> bases from 3'/right end of reads (0)
72
73       --trim-to  [3:|5:]<int> trim reads exceeding <int> bases from either 3'
74       or 5' end
75              If the read end is not specified then it defaults to 3 (0)
76
77       --phred33
78              qualities are Phred+33 (default)
79
80       --phred64
81              qualities are Phred+64
82
83       --int-quals
84              qualities encoded as space-delimited integers
85
86       Presets:
87              Same as:
88
89              For --end-to-end:
90
91       --very-fast            -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
92
93       --fast                 -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
94
95       --sensitive            -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
96
97       --very-sensitive       -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
98
99              For --local:
100
101       --very-fast-local      -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
102
103       --fast-local           -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
104
105       --sensitive-local      -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
106
107       --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
108
109              Alignment:
110
111       -N <int>
112              max # mismatches in seed alignment; can be 0 or 1 (0)
113
114       -L <int>
115              length of seed substrings; must be >3, <32 (22)
116
117       -i <func>
118              interval between seed substrings w/r/t read len (S,1,1.15)
119
120       --n-ceil <func>
121              func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
122
123       --dpad <int>
124              include <int> extra ref chars on sides of DP table (15)
125
126       --gbar <int>
127              disallow gaps within <int> nucs of read extremes (4)
128
129       --ignore-quals
130              treat all quality values as 30 on Phred scale (off)
131
132       --nofw do not align forward (original) version of read (off)
133
134       --norc do not align reverse-complement version of read (off)
135
136       --no-1mm-upfront
137              do not allow 1 mismatch alignments before attempting to scan for
138              the optimal seeded alignments
139
140       --end-to-end
141              entire read must align; no clipping (on)
142
143              OR
144
145       --local
146              local alignment; ends might be soft clipped (off)
147
148              Scoring:
149
150       --ma <int>
151              match bonus (0 for --end-to-end, 2 for --local)
152
153       --mp <int>
154              max penalty for mismatch; lower qual = lower penalty (6)
155
156       --np <int>
157              penalty for non-A/C/G/Ts in read/ref (1)
158
159       --rdg <int>,<int>
160              read gap open, extend penalties (5,3)
161
162       --rfg <int>,<int>
163              reference gap open, extend penalties (5,3)
164
165       --score-min <func> min acceptable alignment score w/r/t read length
166              (G,20,8 for local, L,-0.6,-0.6 for end-to-end)
167
168              Reporting:
169
170       (default)
171              look for multiple alignments, report best, with MAPQ
172
173              OR
174
175       -k <int>
176              report up to <int> alns per read; MAPQ not meaningful
177
178              OR
179
180       -a/--all
181              report all alignments; very slow, MAPQ not meaningful
182
183              Effort:
184
185       -D <int>
186              give up extending after <int> failed extends in a row (15)
187
188       -R <int>
189              for reads w/ repetitive seeds, try <int> sets of seeds (2)
190
191              Paired-end:
192
193       -I/--minins <int>
194              minimum fragment length (0)
195
196       -X/--maxins <int>
197              maximum fragment length (500)
198
199       --fr/--rf/--ff     -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
200
201       --no-mixed
202              suppress unpaired alignments for paired reads
203
204       --no-discordant
205              suppress discordant alignments for paired reads
206
207       --dovetail
208              concordant when mates extend past each other
209
210       --no-contain
211              not concordant when one mate alignment contains other
212
213       --no-overlap
214              not concordant when mates overlap at all
215
216              BAM:
217
218       --align-paired-reads  Bowtie2  will,  by  default, attempt to align un‐
219       paired BAM reads.
220              Use this option to align paired-end reads instead.
221
222       --preserve-tags
223              Preserve tags from the original BAM record by appending them  to
224              the end of the corresponding SAM output.
225
226              Output:
227
228       -t/--time
229              print wall-clock time taken by search phases
230
231       --un <path>
232              write unpaired reads that didn't align to <path>
233
234       --al <path>
235              write unpaired reads that aligned at least once to <path>
236
237       --un-conc <path>
238              write pairs that didn't align concordantly to <path>
239
240       --al-conc <path>
241              write pairs that aligned concordantly at least once to <path>
242
243              (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the
244              option name, e.g.  --un-gz <path>, to gzip compress  output,  or
245              add '-bz2' to bzip2 compress output.)
246
247       --quiet
248              print nothing to stderr except serious errors
249
250       --met-file <path>
251              send metrics to file at <path> (off)
252
253       --met-stderr
254              send metrics to stderr (off)
255
256       --met <int>
257              report internal counters & metrics every <int> secs (1)
258
259       --no-unal
260              suppress SAM records for unaligned reads
261
262       --no-head
263              suppress header lines, i.e. lines starting with @
264
265       --no-sq
266              suppress @SQ header lines
267
268       --rg-id <text>
269              set read group id, reflected in @RG line and RG:Z: opt field
270
271       --rg <text>
272              add  <text>  ("lab:value") to @RG line of SAM header.  Note: @RG
273              line only printed when --rg-id is set.
274
275       --omit-sec-seq
276              put '*' in SEQ and QUAL fields for secondary alignments.
277
278       --sam-no-qname-trunc Suppress standard behavior of truncating  readname
279       at first whitespace
280              at the expense of generating non-standard SAM.
281
282       --xeq  Use  '='/'X',  instead  of 'M,' to specify matches/mismatches in
283              SAM record.
284
285       --soft-clipped-unmapped-tlen Exclude soft-clipped bases when  reporting
286              TLEN
287
288              Performance:
289
290       -p/--threads <int> number of alignment threads to launch (1)
291
292       --reorder
293              force SAM output order to match order of input reads
294
295       --mm   use memory-mapped I/O for index; many 'bowtie's can share
296
297              Other:
298
299       --qc-filter
300              filter out reads that are bad according to QSEQ filter
301
302       --seed <int>
303              seed for random number generator (0)
304
305       --non-deterministic  seed  rand. gen. arbitrarily instead of using read
306              attributes
307
308       --version
309              print version information and quit
310
311       -h/--help
312              print this usage message
313
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316bowtie2 2.4.1                      July 2022                        BOWTIE2(1)