To use this tool your dataset needs to be in the csfasta (as ABI SOLiD color-space sequences) format. Click pencil icon next to your dataset to set the datatype to csfasta.

What it does

SHRiMP (SHort Read Mapping Package) is a software package for aligning genomic reads against a target genome.

Input formats

A multiple color-space file, for example:

>2_263_779_F3
T132032030200202202003211302222202230022110222

Outputs

The tool returns the default SHRiMP output:

   1                      2               3         4        5        6       7      8      9      10
--------------------------------------------------------------------------------------------------------------------
  >2_263_779_F3   Streptococcus_suis      +       814344  814388      1      45      45    3660    8x19x3x2x6x4x3

where:

 1. (>2_263_779_F3)        - Read id
 2. (Streptococcus_suis)   - Reference sequence id
 3. (+)                    - Strand of the read
 4. (814344)               - Start position of the alignment in the reference
 5. (814388)               - End position of the alignment in the reference
 6. (1)                    - Start position of the alignment in the read
 7. (45)                   - End position of the alignment in the read
 8. (45)                   - Length of the read
 9. (3660)                 - Score
10. (8x19x3x2x6x4x3)       - Edit string

SHRiMP parameter list

The commonly used parameters with default value setting:

-s    Spaced Seed                             (default: 111111011111)
      The spaced seed is a single contiguous string of 0's and 1's.
      0's represent wildcards, or positions which will always be
      considered as matching, whereas 1's dictate positions that
      must match. A string of all 1's will result in a simple kmer scan.
-n    Seed Matches per Window                 (default: 2)
      The number of seed matches per window dictates how many seeds
      must match within some window length of the genome before that
      region is considered for Smith-Waterman alignment. A lower
      value will increase sensitivity while drastically increasing
      running time. Higher values will have the opposite effect.
-t    Seed Hit Taboo Length                   (default: 4)
      The seed taboo length specifies how many target genome bases
      or colours must exist prior to a previous seed match in order
      to count another seed match as a hit.
-9    Seed Generation Taboo Length            (default: 0)

-w    Seed Window Length                      (default: 115.00%)
      This parameter specifies the genomic span in bases (or colours)
      in which *seed_matches_per_window* must exist before the read
      is given consideration by the Simth-Waterman alignment machinery.
-o    Maximum Hits per Read                   (default: 100)
      This parameter specifies how many hits to remember for each read.
      If more hits are encountered, ones with lower scores are dropped
      to make room.
-r    Maximum Read Length                     (default: 1000)
      This parameter specifies the maximum length of reads that will
      be encountered in the dataset. If larger reads than the default
      are used, an appropriate value must be passed to *rmapper*.
-d    Kmer Std. Deviation Limit               (default: -1 [None])
      This option permits pruning read kmers, which occur with
      frequencies greater than *kmer_std_dev_limit* standard
      deviations above the average. This can shorten running
      time at the cost of some sensitivity.
      *Note*: A negative value disables this option.
-m    S-W Match Value                         (default: 100)
      The value applied to matches during the Smith-Waterman score calculation.
-i    S-W Mismatch Value                      (default: -150)
      The value applied to mismatches during the Smith-Waterman
      score calculation.
-g    S-W Gap Open Penalty (Reference)        (default: -400)
      The value applied to gap opens along the reference sequence
      during the Smith-Waterman score calculation.
      *Note*: Note that for backward compatibility, if -g is set
      and -q is not set, the gap open penalty for the query will
      be set to the same value as specified for the reference.
-q    S-W Gap Open Penalty (Query)            (default: -400)
      The value applied to gap opens along the query sequence during
      the Smith-Waterman score calculation.
-e    S-W Gap Extend Penalty (Reference)      (default: -70)
      The value applied to gap extends during the Smith-Waterman score calculation.
      *Note*: Note that for backward compatibility, if -e is set
      and -f is not set, the gap exten penalty for the query will
      be set to the same value as specified for the reference.
-f    S-W Gap Extend Penalty (Query)          (default: -70)
      The value applied to gap extends during the Smith-Waterman score calculation.
-x
-h    S-W Full Hit Threshold                  (default: 68.00%)
      In letter-space, this parameter determines the threshold
      score for both vectored and full Smith-Waterman alignments.
      Any values less than this quantity will be thrown away.
      *Note* This option differs slightly in meaning between letter-space and color-space.
-v