[2] | 1 | <tool id="shrimp_color_wrapper" name="SHRiMP for Color-space" version="1.0.0"> |
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| 2 | <description>reads mapping against reference sequence </description> |
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| 3 | <command interpreter="python"> |
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| 4 | #if $param.skip_or_full=="skip" #shrimp_color_wrapper.py $input_target $input_query $output1 |
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| 5 | #else #shrimp_color_wrapper.py $input_target $input_query $output1 $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_crossover_penalty $param.sw_full_hit_threshold $param.sw_vector_hit_threshold |
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| 6 | #end if# |
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| 7 | </command> |
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| 8 | <inputs> |
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| 9 | <page> |
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| 10 | <param name="input_query" type="data" format="csfasta" label="Align sequencing reads" help="No dataset? Read tip below"/> |
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| 11 | <param name="input_target" type="data" format="fasta" label="against reference" /> |
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| 12 | <conditional name="param"> |
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| 13 | <param name="skip_or_full" type="select" label="SHRiMP settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full List"> |
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| 14 | <option value="skip">Commonly used</option> |
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| 15 | <option value="full">Full Parameter List</option> |
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| 16 | </param> |
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| 17 | <when value="skip" /> |
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| 18 | <when value="full"> |
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| 19 | <param name="spaced_seed" type="text" size="30" value="1111001111" label="Spaced Seed" /> |
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| 20 | <param name="seed_matches_per_window" type="integer" size="5" value="2" label="Seed Matches per Window" /> |
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| 21 | <param name="seed_hit_taboo_length" type="integer" size="5" value="4" label="Seed Hit Taboo Length" /> |
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| 22 | <param name="seed_generation_taboo_length" type="integer" size="5" value="0" label="Seed Generation Taboo Length" /> |
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| 23 | <param name="seed_window_length" type="float" size="10" value="115.0" label="Seed Window Length" help="in percentage"/> |
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| 24 | <param name="max_hits_per_read" type="integer" size="10" value="100" label="Maximum Hits per Read" /> |
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| 25 | <param name="max_read_length" type="integer" size="10" value="1000" label="Maximum Read Length" /> |
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| 26 | <param name="kmer" type="integer" size="10" value="-1" label="Kmer Std. Deviation Limit" help="-1 as None"/> |
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| 27 | <param name="sw_match_value" type="integer" size="10" value="100" label="S-W Match Value" /> |
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| 28 | <param name="sw_mismatch_value" type="integer" size="10" value="-150" label="S-W Mismatch Value" /> |
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| 29 | <param name="sw_gap_open_ref" type="integer" size="10" value="-400" label="S-W Gap Open Penalty (Reference)" /> |
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| 30 | <param name="sw_gap_open_query" type="integer" size="10" value="-400" label="S-W Gap Open Penalty (Query)" /> |
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| 31 | <param name="sw_gap_ext_ref" type="integer" size="10" value="-70" label="S-W Gap Extend Penalty (Reference)" /> |
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| 32 | <param name="sw_gap_ext_query" type="integer" size="10" value="-70" label="S-W Gap Extend Penalty (Query)" /> |
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| 33 | <param name="sw_crossover_penalty" type="integer" size="10" value="-140" label="S-W Crossover Penalty" /> |
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| 34 | <param name="sw_full_hit_threshold" type="float" size="10" value="68.0" label="S-W Full Hit Threshold" help="in percentage"/> |
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| 35 | <param name="sw_vector_hit_threshold" type="float" size="10" value="60.0" label="S-W Vector Hit Threshold" help="in percentage"/> |
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| 36 | </when> |
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| 37 | </conditional> |
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| 38 | </page> |
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| 39 | </inputs> |
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| 40 | <outputs> |
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| 41 | <data name="output1" format="tabular"/> |
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| 42 | </outputs> |
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| 43 | <requirements> |
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| 44 | <requirement type="binary">rmapper-cs</requirement> |
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| 45 | </requirements> |
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| 46 | <tests> |
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| 47 | <test> |
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| 48 | <param name="skip_or_full" value="skip" /> |
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| 49 | <param name="input_target" value="Ssuis.fasta" ftype="fasta" /> |
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| 50 | <param name="input_query" value="shrimp_cs_test1.csfasta" ftype="csfasta"/> |
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| 51 | <output name="output1" file="shrimp_cs_test1.out" /> |
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| 52 | </test> |
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| 53 | </tests> |
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| 54 | <help> |
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| 55 | |
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| 56 | .. class:: warningmark |
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| 57 | |
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| 58 | 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*. |
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| 59 | |
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| 60 | |
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| 61 | ----- |
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| 62 | |
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| 63 | **What it does** |
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| 64 | |
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| 65 | SHRiMP (SHort Read Mapping Package) is a software package for aligning genomic reads against a target genome. |
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| 66 | |
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| 67 | |
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| 68 | ----- |
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| 69 | |
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| 70 | **Input formats** |
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| 71 | |
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| 72 | A multiple color-space file, for example:: |
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| 73 | |
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| 74 | >2_263_779_F3 |
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| 75 | T132032030200202202003211302222202230022110222 |
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| 76 | |
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| 77 | |
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| 78 | ----- |
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| 79 | |
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| 80 | **Outputs** |
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| 81 | |
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| 82 | The tool returns the default SHRiMP output:: |
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| 83 | |
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| 84 | |
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| 85 | 1 2 3 4 5 6 7 8 9 10 |
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| 86 | -------------------------------------------------------------------------------------------------------------------- |
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| 87 | >2_263_779_F3 Streptococcus_suis + 814344 814388 1 45 45 3660 8x19x3x2x6x4x3 |
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| 88 | |
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| 89 | where:: |
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| 90 | |
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| 91 | 1. (>2_263_779_F3) - Read id |
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| 92 | 2. (Streptococcus_suis) - Reference sequence id |
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| 93 | 3. (+) - Strand of the read |
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| 94 | 4. (814344) - Start position of the alignment in the reference |
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| 95 | 5. (814388) - End position of the alignment in the reference |
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| 96 | 6. (1) - Start position of the alignment in the read |
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| 97 | 7. (45) - End position of the alignment in the read |
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| 98 | 8. (45) - Length of the read |
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| 99 | 9. (3660) - Score |
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| 100 | 10. (8x19x3x2x6x4x3) - Edit string |
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| 101 | |
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| 102 | |
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| 103 | ----- |
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| 104 | |
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| 105 | **SHRiMP parameter list** |
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| 106 | |
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| 107 | The commonly used parameters with default value setting:: |
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| 108 | |
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| 109 | -s Spaced Seed (default: 111111011111) |
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| 110 | The spaced seed is a single contiguous string of 0's and 1's. |
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| 111 | 0's represent wildcards, or positions which will always be |
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| 112 | considered as matching, whereas 1's dictate positions that |
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| 113 | must match. A string of all 1's will result in a simple kmer scan. |
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| 114 | -n Seed Matches per Window (default: 2) |
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| 115 | The number of seed matches per window dictates how many seeds |
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| 116 | must match within some window length of the genome before that |
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| 117 | region is considered for Smith-Waterman alignment. A lower |
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| 118 | value will increase sensitivity while drastically increasing |
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| 119 | running time. Higher values will have the opposite effect. |
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| 120 | -t Seed Hit Taboo Length (default: 4) |
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| 121 | The seed taboo length specifies how many target genome bases |
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| 122 | or colours must exist prior to a previous seed match in order |
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| 123 | to count another seed match as a hit. |
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| 124 | -9 Seed Generation Taboo Length (default: 0) |
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| 125 | |
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| 126 | -w Seed Window Length (default: 115.00%) |
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| 127 | This parameter specifies the genomic span in bases (or colours) |
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| 128 | in which *seed_matches_per_window* must exist before the read |
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| 129 | is given consideration by the Simth-Waterman alignment machinery. |
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| 130 | -o Maximum Hits per Read (default: 100) |
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| 131 | This parameter specifies how many hits to remember for each read. |
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| 132 | If more hits are encountered, ones with lower scores are dropped |
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| 133 | to make room. |
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| 134 | -r Maximum Read Length (default: 1000) |
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| 135 | This parameter specifies the maximum length of reads that will |
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| 136 | be encountered in the dataset. If larger reads than the default |
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| 137 | are used, an appropriate value must be passed to *rmapper*. |
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| 138 | -d Kmer Std. Deviation Limit (default: -1 [None]) |
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| 139 | This option permits pruning read kmers, which occur with |
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| 140 | frequencies greater than *kmer_std_dev_limit* standard |
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| 141 | deviations above the average. This can shorten running |
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| 142 | time at the cost of some sensitivity. |
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| 143 | *Note*: A negative value disables this option. |
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| 144 | -m S-W Match Value (default: 100) |
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| 145 | The value applied to matches during the Smith-Waterman score calculation. |
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| 146 | -i S-W Mismatch Value (default: -150) |
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| 147 | The value applied to mismatches during the Smith-Waterman |
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| 148 | score calculation. |
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| 149 | -g S-W Gap Open Penalty (Reference) (default: -400) |
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| 150 | The value applied to gap opens along the reference sequence |
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| 151 | during the Smith-Waterman score calculation. |
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| 152 | *Note*: Note that for backward compatibility, if -g is set |
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| 153 | and -q is not set, the gap open penalty for the query will |
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| 154 | be set to the same value as specified for the reference. |
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| 155 | -q S-W Gap Open Penalty (Query) (default: -400) |
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| 156 | The value applied to gap opens along the query sequence during |
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| 157 | the Smith-Waterman score calculation. |
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| 158 | -e S-W Gap Extend Penalty (Reference) (default: -70) |
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| 159 | The value applied to gap extends during the Smith-Waterman score calculation. |
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| 160 | *Note*: Note that for backward compatibility, if -e is set |
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| 161 | and -f is not set, the gap exten penalty for the query will |
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| 162 | be set to the same value as specified for the reference. |
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| 163 | -f S-W Gap Extend Penalty (Query) (default: -70) |
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| 164 | The value applied to gap extends during the Smith-Waterman score calculation. |
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| 165 | -x |
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| 166 | -h S-W Full Hit Threshold (default: 68.00%) |
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| 167 | In letter-space, this parameter determines the threshold |
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| 168 | score for both vectored and full Smith-Waterman alignments. |
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| 169 | Any values less than this quantity will be thrown away. |
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| 170 | *Note* This option differs slightly in meaning between letter-space and color-space. |
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| 171 | -v |
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| 172 | |
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| 173 | |
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| 174 | ----- |
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| 175 | |
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| 176 | **Reference** |
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| 177 | |
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| 178 | **SHRiMP**: Stephen M. Rumble, Michael Brudno, Phil Lacroute, Vladimir Yanovsky, Marc Fiume, Adrian Dalca. shrimp at cs dot toronto dot edu. |
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| 179 | |
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| 180 | </help> |
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| 181 | </tool> |
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