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bowtie-debug - Online in the Cloud

Run bowtie-debug in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command bowtie-debug 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


bowtie - ultrafast memory-efficient short read aligner

DESCRIPTION


Usage: bowtie [options]* <ebwt> {-1 <m1> -2 <m2> | --12 <r> | <s>} [<hit>]

<m1> Comma-separated list of files containing upstream mates (or the sequences
themselves, if -c is set) paired with mates in <m2>

<m2> Comma-separated list of files containing downstream mates (or the sequences
themselves if -c is set) paired with mates in <m1>

<r> Comma-separated list of files containing Crossbow-style reads. Can be a mixture of
paired and unpaired. Specify "-" for stdin.

<s> Comma-separated list of files containing unpaired reads, or the sequences
themselves, if -c is set. Specify "-" for stdin.

<hit> File to write hits to (default: stdout)

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

-f query input files are (multi-)FASTA .fa/.mfa

-r query input files are raw one-sequence-per-line

-c query sequences given on cmd line (as <mates>, <singles>)

-C reads and index are in colorspace

-Q/--quals <file>
QV file(s) corresponding to CSFASTA inputs; use with -f -C

--Q1/--Q2 <file>
same as -Q, but for mate files 1 and 2 respectively

-s/--skip <int>
skip the first <int> reads/pairs in the input

-u/--qupto <int>
stop after first <int> reads/pairs (excl. skipped reads)

-5/--trim5 <int>
trim <int> bases from 5' (left) end of reads

-3/--trim3 <int>
trim <int> bases from 3' (right) end of reads

--phred33-quals
input quals are Phred+33 (default)

--phred64-quals
input quals are Phred+64 (same as --solexa1.3-quals)

--solexa-quals
input quals are from GA Pipeline ver. < 1.3

--solexa1.3-quals
input quals are from GA Pipeline ver. >= 1.3

--integer-quals
qualities are given as space-separated integers (not ASCII)

--large-index
force usage of a 'large' index, even if a small one is present

Alignment:
-v <int>
report end-to-end hits w/ <=v mismatches; ignore qualities

or

-n/--seedmms <int> max mismatches in seed (can be 0-3, default: -n 2)

-e/--maqerr <int>
max sum of mismatch quals across alignment for -n (def: 70)

-l/--seedlen <int> seed length for -n (default: 28)

--nomaqround
disable Maq-like quality rounding for -n (nearest 10 <= 30)

-I/--minins <int>
minimum insert size for paired-end alignment (default: 0)

-X/--maxins <int>
maximum insert size for paired-end alignment (default: 250)

--fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (default: --fr)

--nofw/--norc
do not align to forward/reverse-complement reference strand

--maxbts <int>
max # backtracks for -n 2/3 (default: 125, 800 for --best)

--pairtries <int>
max # attempts to find mate for anchor hit (default: 100)

-y/--tryhard
try hard to find valid alignments, at the expense of speed

--chunkmbs <int>
max megabytes of RAM for best-first search frames (def: 64)

Reporting:
-k <int>
report up to <int> good alignments per read (default: 1)

-a/--all
report all alignments per read (much slower than low -k)

-m <int>
suppress all alignments if > <int> exist (def: no limit)

-M <int>
like -m, but reports 1 random hit (MAPQ=0); requires --best

--best hits guaranteed best stratum; ties broken by quality

--strata
hits in sub-optimal strata aren't reported (requires --best)

Output:
-t/--time
print wall-clock time taken by search phases

-B/--offbase <int> leftmost ref offset = <int> in bowtie output (default: 0)

--quiet
print nothing but the alignments

--refout
write alignments to files refXXXXX.map, 1 map per reference

--refidx
refer to ref. seqs by 0-based index rather than name

--al <fname>
write aligned reads/pairs to file(s) <fname>

--un <fname>
write unaligned reads/pairs to file(s) <fname>

--max <fname>
write reads/pairs over -m limit to file(s) <fname>

--suppress <cols>
suppresses given columns (comma-delim'ed) in default output

--fullref
write entire ref name (default: only up to 1st space)

Colorspace:
--snpphred <int>
Phred penalty for SNP when decoding colorspace (def: 30)

or

--snpfrac <dec>
approx. fraction of SNP bases (e.g. 0.001); sets --snpphred

--col-cseq
print aligned colorspace seqs as colors, not decoded bases

--col-cqual
print original colorspace quals, not decoded quals

--col-keepends
keep nucleotides at extreme ends of decoded alignment

SAM:
-S/--sam
write hits in SAM format

--mapq <int>
default mapping quality (MAPQ) to print for SAM alignments

--sam-nohead
supppress header lines (starting with @) for SAM output

--sam-nosq
supppress @SQ header lines for SAM output

--sam-RG <text>
add <text> (usually "lab=value") to @RG line of SAM header

Performance:
-o/--offrate <int> override offrate of index; must be >= index's offrate

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

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

--shmem
use shared mem for index; many 'bowtie's can share

Other:
--seed <int>
seed for random number generator

--verbose
verbose output (for debugging)

--version
print version information and quit

-h/--help
print this usage message

64-bit Built on lgw01-11 Thu Nov 26 11:11:48 UTC 2015 Compiler: gcc version 5.2.1 20151123
(Ubuntu 5.2.1-25ubuntu1) Options: -O3 -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro Sizeof {int, long,
long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

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