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Type:
Improvement
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Status: Closed
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Priority:
Major
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Resolution: Fixed
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Affects Version/s: virogenesis
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Fix Version/s: 1.31
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Labels:
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Story Points:3
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Epic Link:
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Sprint:DEV-30-5, DEV-30-6
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Affect Type:Userdefined
See also the DIAMOND manual.
Add parameters to the "Classify Sequences with DIAMOND" element specified below. Note that not all parameters available are listed.
| # | Parameter | Description | Value in GUI | Default value |
|---|---|---|---|---|
| 1 | Database | The parameter is already present, just leave it as it is. | Leave it the same. | Leave it the same for now. |
| 2 | Genetic code | Genetic code used for translation of query sequences (--query-gencode). | See combo box for similar parameter in the "ORF Marker" element. | "1. The Standard Genetic Code" |
| 3 | Sensitive mode | The sensitive modes (--sensitive, --more-sensitive) are generally recommended for aligning longer sequences. The default mode is mainly designed for short read alignment, i.e. finding significant matches of >50 bits on 30-40aa fragments. | A combo box with values: "Default", "Sensitive", "More sensitive" | "Default" |
| 4 | Frameshift | Penalty for frameshift in DNA-vs-protein alignments. Values around 15 are reasonable for this parameter. Enabling this feature will have the aligner tolerate missing bases in DNA sequences and is most recommended for long, error-prone sequences like MinION reads. | A spin box with values "Skipped" and non-negative integer values. | "Skipped"(0) |
| 5 | Expected value | Maximum expected value to report an alignment. | A spin box with non-negative real values | 0.001 |
| 6 | Matrix | Scoring matrix (--matrix). | A combo box with the following values: "BLOSUM45", "BLOSUM50", "BLOSUM62", "BLOSUM80", "BLOSUM90", "PAM250", "PAM70", "PAM30". | "BLOSUM62"" |
| 7 | Gap open penalty | Gap open penalty (--gapopen). | A spin box with values "Default" and other non-negative integer values | "Default"(-1) |
| 8 | Gap extension penalty | Gap extension penalty (--gapextend). | A spin box with values "Default" and other non-negative integer values | "Default"(-1) |
| 9 | Number of threads | Number of CPU threads (--treads). | A spin box with values from 1 to the number of available cores. | Use the value from the Application Settings (the "Optimize for CPU count" option). |
| 10 | Block size | Block size in billions of sequence letters to be processed at a time (--block-size). This is the main parameter for controlling the program’s memory usage. Bigger numbers will increase the use of memory and temporary disk space, but also improve performance. The program can be expected to use roughly six times this number of memory (in GB). |
A spin box with values "Default" and other non-negative real numbers. Zero means program default. | 2.0 |
| 11 | Index chunks | The number of chunks for processing the seed index (--index-chunks). This option can be additionally used to tune the performance. It is recommended to set this to 1 on a high memory server, which will increase performance and memory usage, but not the usage of temporary disk space. | A spin box with non-negative integer values | 4 |
| 12 | Output file | See |
See |
See |