Generates a QC report on raw sequence data.
Author: Brabaham Institute
Marc-Danie Nazaire, email@example.com
Algorithm Version: 0.10.1
|input file *||A raw sequence file - .fastq, .sam, .bam.|
|input format||Bypasses the normal sequence file format detection and forces the program to use the specified format. Valid formats are bam,sam,bam_mapped,sam_mapped and fastq|
|contaminant file||Specifies a non-default file which contains the list of contaminants to screen overrepresented sequences against. The file must contain sets of named contaminants in the form name[tab]sequence. Lines prefixed with a hash will be ignored.|
|kmer size *||Specifies the length of Kmer to look for in the Kmer content module. Specified Kmer length must be between 2 and 10. Default length is 5.|
|extract output||Whether to output an uncompressed version of the report. Set this to yes to view the report directly from within GenePattern.|
* - required
An example of a report from a good Illumina dataset can be found here.
An example of a report from a bad Illumina dataset can be found here.