---
description: What you need in order to operate the tool.
---

# Preparation

If you managed to successfully run our [toy example](https://app.gitbook.com/@yoav-orlev/s/solqc/~/edit/drafts/-LeH9rr_1wEsAw7JVyPY/getting-started/toy-example), you probably noticed you were requested two input files and to fill out the **Library Configurations**. In this section, we go into more details about these files.

#### Design File&#x20;

This could be one of two options:

1. A design file, in a csv format containing 2 columns : \[barcode, variant]
   * barcode - a sequence identifier for the variant. \[Needed for matching between a read and a variant].
   * variant - the complete variant sequence. \[Needed for the alignment to analyse mismatches and indel's].\

2. IUPAC string.

#### Library Configuration

These are the different configurations that can be tuned according to your library:\


* **prefix** : If supplied will remove all reads not starting with the supplied sequence.
* **suffix** : If supplied will remove all reads not ending with the supplied sequence.
*   **length** : If supplied and set to a value above 0 will only leave reads with \


    ```
    length - 5 <= len(read) <= length + 5
    ```
* **barcode\_start** : Start position of the barcode.
* **barcode\_end** : End position of the barcode.
* **barcode\_tolerance** : If supplied will allow barcodes with the amount of errors provided.

#### Reads File/s

A fastq file containing sequenced reads.
