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bowtie2-align-l - ultrafast and memory-efficient backend tool for aligning sequencing
reads to long reference sequences


Bowtie 2 version 2.2.6 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)


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

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.

<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)

-q query input files are FASTQ .fq/.fastq (default)

--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

-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)

qualities are Phred+33 (default)

qualities are Phred+64

qualities encoded as space-delimited integers

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

-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)

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)

do not allow 1 mismatch alignments before attempting to scan for the optimal seeded

entire read must align; no clipping (on)


local alignment; ends might be soft clipped (off)

--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)

look for multiple alignments, report best, with MAPQ


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


report all alignments; very slow, MAPQ not meaningful

-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)


-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)

suppress unpaired alignments for paired reads

suppress discordant alignments for paired reads

not concordant when mates extend past each other

not concordant when one mate alignment contains other

not concordant when mates overlap at all

print wall-clock time taken by search phases

print nothing to stderr except serious errors

--met-file <path>
send metrics to file at <path> (off)

send metrics to stderr (off)

--met <int>
report internal counters & metrics every <int> secs (1)

supppress SAM records for unaligned reads

supppress header lines, i.e. lines starting with @

supppress @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.

put '*' in SEQ and QUAL fields for secondary alignments.

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

force SAM output order to match order of input reads

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

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

print version information and quit

print this usage message

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