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.

CommandoradoraFuseora 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 softwareoradoraFuseora 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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