What it does

See the TMAP manual for more information.

It combines multiple mapping algorithms to give sensitive and accurate alignments quickly. It uses three core algorithms, BWA-short, BWA-long, and a variant of the SSAHA algorithm. These algorithms are described in the following publications:

• Li, H. and Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754–1760.
• Li, H. and Durbin, R. (2010). Fast and accurate long-read alignment with Burrows-Wheeler
• Ning, Z., Cox, A., and Mullikin, J. (2001). SSAHA: a fast search method for large DNA databases. Genome Res., 11, 1725–1729.

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

TMAP accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files. TMAP also accepts SFF 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:VALU

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

TMAP settings

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