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Toolbox for generic NGS analyses

SUMMARY

QC control

Configuration file used and validated to control data quality:

Mapping

Configuration file used and validated to map FASTQ data:

SNP detection and cleaning

Configuration file used and validated to detect polymorphisms (SNP and INDEL):

Differential genes expression

Configuration file used and validated to perform differential genes expression analysis:

Demultiplexing RADseq data

Configuration file used and validated to perform demultiplexing:

Assembly

Configuration file used and validated to perform assembly:

Structural Variations

Configuration file used and validated to perform SV detection:

BED tools

Configuration file used and validated to perform BEDtools: