# Pipeline

In order to produce the report, the user needs to input a design file (csv) and a reads file or files representing the NGS results (typically fastq) on a library which is based on variants represented in the design file. 

Then the following pipeline will take place: 

1. **Prepossessing** : The input reads will be filtered so only valid sequences will stay for further analysis. What constitutes as a valid read can be configured by the user, using parameters such as sequence prefix and sequence length. 
2. **Matching** : Each sequence will be matched to a corresponding variant. The matching can be done by different strategies. We are planning to implement the following approaches: 
   1. *Barcode matching* : If the library has a barcode assigned to each variant we will use that barcode to match each read with a tun-able tolerance for the matching. 
   2. *Edit distance* : Calculates edit distance between an input read and, in principle, all the variants. The variant with the lowest edit distance will be selected as the matched one. 
3. **Alignment** : We then align each read to its corresponding variant and build the CIGAR path. 
4. **Analysis** : We then use the collected data (match, alignment) to calculate different statistics mentioned in the synthetic library. 
5. **Report Generation**: Finally, the calculated statistics are reported to the end user in a clean and accessible manner.

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