Version Differences for Manual2
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(→Commands and configuration)
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(→CISA.py)
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| Line 58: | |||
| blastn=path/blastn <font color=blue> Please modify the "path" into the 安裝路徑.</font> | blastn=path/blastn <font color=blue> Please modify the "path" into the 安裝路徑.</font> | ||
| - | genome | + | #genome<br/>We suggest to use the longest length which is between attended contigs as genome variable.<br/>The break point of CISA will be set to 1.1 * genome variable. |
| + | #infile<br/>File name with input. | ||
| - | We suggest to use the longest length which is between attended contigs as genome variable.<br> | + | #nucmer<br/>Executive file for nucmer. If nucmer has beed set into the path, nucmer variable can be skipped. |
| - | The break point of CISA will be set to 1.1 * genome variable. | + | #makeblastdb<br/>Executive file for makeblastdb. If makeblastdb has beed set into the path, makeblastdb variable can be skipped. |
| + | #blastn<br/>Executive file for blastn. If blastn has beed set into the path, blastn variable can be skipped. | ||
| - | infile<br> | + | #CISA<br/>Home directory of CISA. |
| - | File name with input. | + | #R2_Gap<br/>Tolerant amount of gap during CISA2 step. |
| - | nucmer<br> | ||
| - | Executive file for nucmer. If nucmer has beed set into the path, nucmer variable can be skipped. | ||
| - | makeblastdb<br> | ||
| - | Executive file for makeblastdb. If makeblastdb has beed set into the path, makeblastdb variable can be skipped. | ||
| - | blastn<br> | ||
| - | Executive file for blastn. If blastn has beed set into the path, blastn variable can be skipped. | ||
| - | CISA<br> | ||
| - | Home directory of CISA. | ||
| - | R2_Gap<br> | ||
| - | Tolerant amount of gap during CISA2 step. | ||
| = Example = | = Example = | ||