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Toolbox for generic NGS analyses

In TOGGLE, we developed also home made tools for different processes. The following functions can be accessed using toggleGenerator.

  1. fastqUtils Tools
  2. checkFormat Tools

fastqUtils Tools

checkFormatByASCIIcontrol

This module checks the FASTQ encoding level (64 or 33 PHRED) of a given file (plain text or gzip). The block provides a log file indicating if the encoding is 33 PHRED or not.


checkFormat Tools

checkFormatFasta

This function checks if a file is really a FASTA file (accepting the degenerated IUPAC code). The block returns a log file indicating if the FASTA file is a correct one and report the lines with errors. Note: the system will stop after 20 errors are found.

checkFormatFastq

This function checks if a file is really a FASTQ file. The block returns a log file indicating if the FASTQ file is a correct one.

checkFormatSamOrBam

This function checks if a file is really a SAM or BAM file. The block returns a log file indicating if the SAM or BAM file is a correct one.

checkFormatVcf

This function checks if a file is really a VCF v4+ file. The block returns a log file indicating if the VCF file is a correct one.