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 2.2.9 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>} [-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.
<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)
--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
--no-dovetail
not 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.
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
Opportunity
Personal Opportunity - Free software gives you access to billions of dollars of software at no cost. Use this software for your business, personal use or to develop a profitable skill. Access to source code provides access to a level of capabilities/information that companies protect though copyrights. Open source is a core component of the Internet and it is available to you. Leverage the billions of dollars in resources and capabilities to build a career, establish a business or change the world. The potential is endless for those who understand the opportunity.
Business Opportunity - Goldman Sachs, IBM and countless large corporations are leveraging open source to reduce costs, develop products and increase their bottom lines. Learn what these companies know about open source and how open source can give you the advantage.
Free Software
Free Software provides computer programs and capabilities at no cost but more importantly, it provides the freedom to run, edit, contribute to, and share the software. The importance of free software is a matter of access, not price. Software at no cost is a benefit but ownership rights to the software and source code is far more significant.
Free Office Software - The Libre Office suite provides top desktop productivity tools for free. This includes, a word processor, spreadsheet, presentation engine, drawing and flowcharting, database and math applications. Libre Office is available for Linux or Windows.
Free Books
The Free Books Library is a collection of thousands of the most popular public domain books in an online readable format. The collection includes great classical literature and more recent works where the U.S. copyright has expired. These books are yours to read and use without restrictions.
Source Code - Want to change a program or know how it works? Open Source provides the source code for its programs so that anyone can use, modify or learn how to write those programs themselves. Visit the GNU source code repositories to download the source.
Education
Study at Harvard, Stanford or MIT - Open edX provides free online courses from Harvard, MIT, Columbia, UC Berkeley and other top Universities. Hundreds of courses for almost all major subjects and course levels. Open edx also offers some paid courses and selected certifications.
Linux Manual Pages - A man or manual page is a form of software documentation found on Linux/Unix operating systems. Topics covered include computer programs (including library and system calls), formal standards and conventions, and even abstract concepts.
