Provided by: bowtie2_2.5.4-1_amd64 
NAME
bowtie2-align-l - ultrafast and memory-efficient backend tool for aligning sequencing
reads to long reference sequences
DESCRIPTION
Bowtie 2 version 2.5.4 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
USAGE
bowtie2-align [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | -b
<bam>} [-S <sam>]
<bt2-idx>
Index filename prefix (minus trailing .X.bt2l). NOTE: Bowtie 1 and Bowtie 2
indexes are not compatible.
<m1> Files with #1 mates, paired with files in <m2>.
<m2> Files with #2 mates, paired with files in <m1>.
<r> Files with unpaired reads.
<i> Files with interleaved paired-end FASTQ/FASTA reads
<bam> Files are unaligned BAM sorted by read name.
<sam> File for SAM output (default: stdout)
<m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be specified
many times. E.g. '-U file1.fq,file2.fq -U file3.fq'.
OPTIONS (defaults in parentheses)
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:
--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
--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