- FASTQ formatted, paired-end raw sequences
- SAM formatted form(generated by other alignment tools)
- List of SNPs, indels formatted as ANNOVAR input format
- Expression profile
- Other intermediate files such as GSNAP alignment output files, total alignment depth (coverage) against the reference genome generated from ‘Base Call' step,
and list of indels before filtering to give researchers room to do their own analysis of interest.
- Run-at-Once and Step-by-Step modes: You can run the whole pipe-line from scratch, or run specific steps only.
- Configure filters: On each step, you may change inherent filter conditions based on your analysis purpose.