Difference between revisions of "Kneaddata"
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(Created page with "Category:SoftwareCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|Kneadata}} |{{#vardefine:url|https://huttenhower.sph.harvard.edu/kneaddata/}...") |
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[[Category:Software]][[Category:Phylogenetics]] | [[Category:Software]][[Category:Phylogenetics]] | ||
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
| − | |{{#vardefine:app| | + | |{{#vardefine:app|kneaddata}} |
|{{#vardefine:url|https://huttenhower.sph.harvard.edu/kneaddata/}} | |{{#vardefine:url|https://huttenhower.sph.harvard.edu/kneaddata/}} | ||
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
| + | * HPC_{{uc:{{#var:app}}}}_JRE - java runtime environment executable directory | ||
| + | * HPC_{{uc:{{#var:app}}}}_DB - kneaddata database directory | ||
<!--Configuration--> | <!--Configuration--> | ||
Latest revision as of 16:09, 8 August 2024
Description
KneadData is a tool designed to perform quality control on metagenomic sequencing data, especially data from microbiome experiments. In these experiments, samples are typically taken from a host in hopes of learning something about the microbial community on the host. However, metagenomic sequencing data from such experiments will often contain a high ratio of host to bacterial reads. This tool aims to perform principled in silico separation of bacterial reads from these “contaminant” reads, be they from the host, from bacterial 16S sequences, or other user-defined sources.
Environment Modules
Run module spider kneaddata to find out what environment modules are available for this application.
System Variables
- HPC_KNEADDATA_DIR - installation directory
- HPC_KNEADDATA_BIN - executable directory
- HPC_KNEADDATA_JRE - java runtime environment executable directory
- HPC_KNEADDATA_DB - kneaddata database directory