short_reads_trim_seq.py $trim $length $output1 $input1 $input2 $sequencing_method_choice.input3 Roche (454) or ABI SOLiD Illumina (Solexa) DO NOT trigger splitting trigger splitting

.. class:: warningmark To use this tool, your dataset needs to be in the *Quality Score* format. Click the pencil icon next to your dataset to set the datatype to *Quality Score* (see below for examples). ----- **What it does** This tool finds high quality segments within sequencing reads generated by by Roche (454), Illumina (Solexa), or ABI SOLiD machines. ----- **Example** Suppose this is your sequencing read:: 5'---------*-------------*------**----3' where **dashes** (-) are HIGH quality bases (above 20) and **asterisks** (*) are LOW quality bases (below 20). If the **Minimal length of contiguous segment** is set to **5** (of course, only for the purposes of this example), the tool will return:: 5'--------- ------------- ------- you can see that the tool simply splits the read on low quality bases and then returns all segments longer than 5. **Note**, that the output of this tool will likely contain higher number of shorter sequences compared to the original input. If we set the **Minimal length of contiguous segment** to **0**, the tool will only return the single longest segment:: -------------