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bowtie2-align-l - Online in the Cloud

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This is the command bowtie2-align-l that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


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

DESCRIPTION


Bowtie 2 version 2.2.6 by Ben Langmead ([email protected], 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.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)


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
supppress SAM records for unaligned reads

--no-head
supppress header lines, i.e. lines starting with @

--no-sq
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.

--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

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