Map with Bowtie for Illumina
Built-ins were indexed using default options
if your genome of interest is not listed - contact Galaxy team
Must have ASCII encoded quality scores
For most mapping needs use Commonly used settings. If you want full control use Full parameter list
Bowtie produces SAM with several lines of header information by default

What it does

Bowtie is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.


Know what you are doing

There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to understand the parameters by carefully reading the documentation and experimenting. Fortunately, Galaxy makes experimenting easy.


Input formats

Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.


A Note on Built-in Reference Genomes

Some genomes have multiple variants. If only one "type" of genome is listed, it is the Full version, which means that everything that came in the original genome data download (possibly with mitochondrial and plasmid DNA added if it wasn't already included). The Full version is available for every genome. Some genomes also come in the Canonical variant, which contains only the "canonical" (well-defined) chromosomes or segments, such as chr1-chr22, chrX, chrY, and chrM for human. Other variations include gender. These will come in the canonical form only, so the general Canonical variant is actually Canonical Female and the other is Canonical Male (identical to female excluding chrX).


Outputs

The output is in SAM format, and has the following columns:

  Column  Description
--------  --------------------------------------------------------
 1 QNAME  Query (pair) NAME
 2 FLAG   bitwise FLAG
 3 RNAME  Reference sequence NAME
 4 POS    1-based leftmost POSition/coordinate of clipped sequence
 5 MAPQ   MAPping Quality (Phred-scaled)
 6 CIGAR  extended CIGAR string
 7 MRNM   Mate Reference sequence NaMe ('=' if same as RNAME)
 8 MPOS   1-based Mate POSition
 9 ISIZE  Inferred insert SIZE
10 SEQ    query SEQuence on the same strand as the reference
11 QUAL   query QUALity (ASCII-33 gives the Phred base quality)
12 OPT    variable OPTional fields in the format TAG:VTYPE:VALUE

The flags are as follows:

  Flag  Description
------  -------------------------------------
0x0001  the read is paired in sequencing
0x0002  the read is mapped in a proper pair
0x0004  the query sequence itself is unmapped
0x0008  the mate is unmapped
0x0010  strand of the query (1 for reverse)
0x0020  strand of the mate
0x0040  the read is the first read in a pair
0x0080  the read is the second read in a pair
0x0100  the alignment is not primary

It looks like this (scroll sideways to see the entire example):

QNAME FLAG    RNAME   POS     MAPQ    CIAGR   MRNM    MPOS    ISIZE   SEQ     QUAL    OPT
HWI-EAS91_1_30788AAXX:1:1:1761:343    4       *       0       0       *       *       0       0       AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG        hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
HWI-EAS91_1_30788AAXX:1:1:1578:331    4       *       0       0       *       *       0       0       GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG        hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh

Bowtie settings

All of the options have a default value. You can change any of them. Most of the options in Bowtie have been implemented here.


Bowtie parameter list

This is an exhaustive list of Bowtie options:

For indexing (bowtie-build):

-a                 No auto behavior. Disable the default behavior where bowtie automatically
                   selects values for --bmax/--bmaxdivn/--dcv/--packed parameters according
                   to the memory available. [off]
--packed           Packing. Use a packed representation for DNA strings. [auto]
--bmax INT         Suffix maximum. The maximum number of suffixes allowed in a block. [auto]
--bmaxdivn INT     Suffix maximum fraction. The maximum number of suffixes allowed in a block
                   expressed as a fraction of the length of the reference. [4]
--dcv INT          Difference-cover sample. Use INT as the period for the difference-cover
                   sample. [1024]
--nodc INT         No difference-cover sample. Disable the difference-cover sample. [off]
-r                 No reference indexes. Do not build the NAME.3.ebwt and NAME.4.ebwt portions
                   of the index. Used only for paired-end alignment. [off]
-o                 Offrate. How many Burrows-Wheeler rows get marked by the indexer. The
                   indexer will mark every 2^INT rows. The marked rows correspond to rows on
                   the genome. [5]
-t INT             Ftab. The lookup table used to calculate an initial Burrows-Wheeler range
                   with respect to the first INT characters of the query. Ftab is 4^INT+1
                   bytes. [10]
--ntoa             N conversion. Convert Ns to As before building the index. Otherwise, Ns are
                   simply excluded from the index and Bowtie will not find alignments that
                   overlap them. [off]
--big              Endianness. Endianness to use when serializing integers to the index file. [off]
--little           Endianness. [--little]
--seed INT         Random seed. Use INT as the seed for the pseudo-random number generator. [off]
--cutoff INT       Cutoff. Index only the first INT bases of the reference sequences (cumulative
                   across sequences) and ignore the rest. [off]

For aligning (bowtie):

-s INT             Skip. Do not align the first INT reads or pairs in the input. [off]
-u INT             Align limit. Only align the first INT reads/pairs from the input. [no limit]
-5 INT             High-quality trim. Trim INT bases from the high-quality (left) end of each
                   read before alignment. [0]
-3 INT             Low-quality trim. Trim INT bases from the low-quality (right) end of each
                   read before alignment. [0]
-n INT             Mismatch seed. Maximum number of mismatches permitted in the seed (defined
                   with seed length option). Can be 0, 1, 2, or 3. [2]
-e INT             Mismatch quality. Maximum permitted total of quality values at mismatched
                   read positions. Bowtie rounds quality values to the nearest 10 and saturates
                   at 30. [70]
-l INT             Seed length. The number of bases on the high-quality end of the read to
                   which the -n ceiling applies. Must be at least 5. [28]
--nomaqround       Suppress MAQ rounding. Values are internally rounded to the nearest 10 and
                   saturate at 30. This options turns off that rounding. [off]
-v INT             MAQ- or SOAP-like alignment policy. This option turns off the default
                   MAQ-like alignment policy in favor of a SOAP-like one. End-to-end alignments
                   with at most INT mismatches. [off]
-I INT             Minimum insert. The minimum insert size for valid paired-end alignments.
                   Does checking on untrimmed reads if -5 or -3 is used. [0]
-X INT             Maximum insert. The maximum insert size for valid paired-end alignments.
                   Does checking on untrimmed reads if -5 or -3 is used. [250]
--fr               Mate orientation. The upstream/downstream mate orientations for a valid
                   paired-end alignment against the forward reference strand. [--fr]
--rf               Mate orientation. [off]
--ff               Mate orientation. [off]
--pairtries INT    Maximum alignment attempts for paired-end data. [100]
--nofw             No forward aligning. Choosing this option means that Bowtie will not attempt
                   to align against the forward reference strand. [off]
--norc             No reverse-complement aligning. Setting this will mean that Bowtie will not
                   attempt to align against the reverse-complement reference strand. [off]
--un FILENAME      Write all reads that could not be aligned to file [off]
--max FILENAME     Write all reads with a number of valid alignments exceeding the limit
                   set with the -m option to file [off]
--maxbts INT       Maximum backtracks. The maximum number of backtracks permitted when aligning
                   a read in -n 2 or -n 3 mode. [125 without --best] [800 with --best]
-y                 Try hard. Try as hard as possible to find valid alignments when they exist,
                   including paired-end alignments. [off]
--chunkmbs INT     Thread memory. The number of megabytes of memory a given thread is given to
                   store path descriptors in --best mode. [32]
-k INT             Valid alignments. The number of valid alignments per read or pair. [off]
-a                 All valid alignments. Choosing this means that all valid alignments per read
                   or pair will be reported. [off]
-m INT             Suppress alignments. Suppress all alignments for a particular read or pair
                   if more than INT reportable alignments exist for it. [no limit]
--best             Best mode. Make Bowtie guarantee that reported singleton alignments are
                   "best" in terms of stratum (the number of mismatches) and quality values at
                   mismatched position. [off]
--strata           Best strata. When running in best mode, report alignments that fall into the
                   best stratum if there are ones falling into more than one. [off]
-o INT             Offrate override. Override the offrate of the index with INT. Some row
                   markings are discarded when index read into memory. INT must be greater than
                   the value used to build the index (default: 5). [off]
--seed INT         Random seed. Use INT as the seed for the pseudo-random number generator. [off]
--snpphred INT     Use INT as the SNP penalty for decoding colorspace alignments. True ratio of
                   SNPs per base in the subject genome. [see --snpfrac]
--snpfrac DEC      Use DEC as the estimated ratio of SNPs per base when decoding colorspace
                   alignments. [0.001]
--col-keepends     Keep the extreme-end nucleotides and qualities when decoding colorspace
                   alignments. [off]