Difference between revisions of "AfterQC"
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Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_MAN - manual directory |
<!--Configuration--> | <!--Configuration--> | ||
Latest revision as of 21:19, 6 December 2019
Description
AfterQC Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair. Currently it supports processing data from HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq...and other Illumina 1.8 or newer formats
Environment Modules
Run module spider afterqc to find out what environment modules are available for this application.
System Variables
- HPC_AFTERQC_DIR - installation directory
- HPC_AFTERQC_BIN - executable directory
- HPC_AFTERQC_MAN - manual directory
Citation
If you publish research that uses afterqc you have to cite it as follows: