Difference between revisions of "ContaVect"
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
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{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 21:05, 6 December 2019
Description
Contavect is a python2.7 object oriented script, developed to quantify and characterize DNA contaminants from gene therapy vector production after NGS sequencing. This automated pipeline can however be used for wider purpose requiring to identify map NGS datasets consisting of a mix of DNA sequences on multiple references. It combine several features such as reference homologies masking, fastq filtering/adapter trimming, short read alignments, SAM file splitting and generating human readable output.
Required Modules
Serial
- gcc/5.2.0
- contavect
System Variables
- HPC_CONTAVECT_DIR - installation directory
Additional Information
The sample config file can be copied from the $HPC_CONTAVECT_CONF
$ cp $HPC_CONTAVECT_CONF .