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 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 catcommand)
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