Difference between revisions of "SeqyClean"
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Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:BioinformaticsCategory:NGS {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|seqyclean}} |{{#vardefine:url|REPLACE}} <!--CONFIGURATION: ...") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|seqyclean}} | |{{#vardefine:app|seqyclean}} | ||
| − | |{{#vardefine:url| | + | |{{#vardefine:url|https://bitbucket.org/izhbannikov/seqyclean}} |
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | Raw data from sequencing machines is not usually completely prepared for analysis since sequences often contain remnants of nucleotides that have been used during DNA library preparation. Such nucleotides can potentially case hurdles during data analysis and hereby need to be removed. In additional, the noise, which is presented as low-quality bases, has serious impact on genome assembly and mapping. We propose SeqyClean, a specialized cleaning pipeline that alleviates these issues. | + | Raw data from sequencing machines is not usually completely prepared for analysis since sequences often contain remnants of nucleotides that have been used during DNA library preparation. Such nucleotides can potentially case hurdles during data analysis and hereby need to be removed. In additional, the noise, which is presented as low-quality bases, has serious impact on genome assembly and mapping. We propose SeqyClean, a specialized cleaning pipeline that alleviates these issues. |
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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| − | < | ||
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{# | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| + | * HPC_{{uc:{{#var:app}}}}_BIN | ||
| + | * HPC_{{uc:{{#var:app}}}}_OBJ | ||
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<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 22:41, 21 August 2022
Description
Raw data from sequencing machines is not usually completely prepared for analysis since sequences often contain remnants of nucleotides that have been used during DNA library preparation. Such nucleotides can potentially case hurdles during data analysis and hereby need to be removed. In additional, the noise, which is presented as low-quality bases, has serious impact on genome assembly and mapping. We propose SeqyClean, a specialized cleaning pipeline that alleviates these issues.
Environment Modules
Run module spider seqyclean to find out what environment modules are available for this application.
System Variables
- HPC_SEQYCLEAN_DIR - installation directory
- HPC_SEQYCLEAN_BIN
- HPC_SEQYCLEAN_OBJ