Preparation

What you need in order to operate the tool.

If you managed to successfully run our 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

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.