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