Input

Input for the pipeline is a directory(-readsdir) containing SE/PE reads and a config file where all the configuration settings for the pipeline are set. This config file settings will be used universally on all samples available in readsdir. An example config file with default parameters are included in the pipeline folder. You can customize this config file and provide it with the -config argument.

Detailed information in section Customizing Config file

Note: Apart from standard Miseq/Hiseq fastq naming extensions (R1_001_final.fastq.gz), other acceptable fastq extensions are: R1.fastq.gz/_R1.fastq.gz, 1_combine.fastq.gz, 1_sequence.fastq.gz, _forward.fastq.gz, _1.fastq.gz/.1.fastq.gz.