> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/ora/product-guides/dragen-ora-helper-suite/troubleshooting.md).

# Troubleshooting

You can use the oraHelper interactive user guide for assistance with common Linux commands, and to help troubleshoot errors encountered when using the different software included in the DRAGEN ORA Helper Suite. For details, refer to [oraHelper Interactive User Guide](/ora/product-guides/dragen-ora-helper-suite/tools.md) section.

## Common Linux Commands

The following table shows common Linux commands that you can use with the DRAGEN ORA Helper Suite software. This list is not exhaustive.

| Command | orad              | oraFuse                                 | ora LD-Preload            |
| ------- | ----------------- | --------------------------------------- | ------------------------- |
| ls      | Not applicable    | Yes                                     | Yes                       |
| cat     | Yes               | Yes                                     | Yes                       |
| head    | Yes               | Yes                                     | Yes                       |
| md5sum  | Yes               | Yes                                     | Yes                       |
| grep    | Yes               | Yes                                     | No                        |
| cp      | Copy \*.fastq.ora | Copy uncompressed FASTQ or \*.fastq.ora | No (use the `cat`command) |
| awk     | Yes               | Yes                                     | Yes                       |
| tail    | Yes               | Yes                                     | Yes                       |
| wc      | Yes               | Yes                                     | Yes                       |
| uniq    | Yes               | Yes                                     | No                        |
| string  | Yes               | Yes                                     | Yes                       |
| sort    | Yes               | Yes                                     | No                        |

## Bioinformatics Software

The DRAGEN ORA Helper Suite software work with some commonly used bioinformatics software. If the bioinformatics software is supported, you can use the oraHelper interactive user guide to help troubleshoot errors with your command. Below is the list of supported bioinformatics software with DRAGEN ORA Helper Suite. It does not limit the use of other thrid-party software.

| Bioinformatics software | orad                  | oraFuse | ora LD-Preload        |
| ----------------------- | --------------------- | ------- | --------------------- |
| BWA v0.7.17             | Yes                   | Yes     | Yes                   |
| Bowtie2 v2.4.2          | Yes                   | Yes     | Yes                   |
| STAR v2.7.8a            | Yes                   | Yes     | Yes                   |
| Minimap2 v2.17          | Yes                   | Yes     | Yes                   |
| DRAGMAP v1.3            | Yes                   | Yes     | No                    |
| FASTQC v0.11.9          | Use std:input command | Yes     | Use std:input command |
| Cutadapt v3.7           | Yes                   | Yes     | No                    |
| SPAdes v3.15.4          | Yes                   | Yes     | No                    |
| LAST v1.25.7            | Yes                   | Yes     | Yes                   |
| Seqkit v0.16.1          | Yes                   | Yes     | No                    |
| Seqtk v1.3              | Yes                   | Yes     | Yes                   |
| Fastp v0.23.1           | Yes                   | Yes     | No                    |


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