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bowtie2-align-s - ultrafast and memory-efficient backend tool for aligning

BOWTIE2-ALIGN-S(1) User Commands BOWTIE2-ALIGN-S(1)

NAME

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

DESCRIPTION

Bowtie 2 version 2.3.3.1 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>} [-S <sam>]
<bt2-idx>
Index filename prefix (minus trailing .X.bt2). 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 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)

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
-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)
--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

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

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
October 2017 bowtie2-align-s 2.3.3.1